Query 023705
Match_columns 278
No_of_seqs 20 out of 22
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 06:02:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023705.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023705hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0154 RNA-binding protein RB 97.9 6.7E-07 1.4E-11 86.5 -3.1 191 66-257 235-437 (573)
2 KOG4509 Uncharacterized conser 89.3 0.69 1.5E-05 42.7 5.0 79 118-196 41-120 (247)
3 TIGR02395 rpoN_sigma RNA polym 88.4 1.6 3.4E-05 42.4 7.1 89 148-236 300-418 (429)
4 PF04552 Sigma54_DBD: Sigma-54 88.2 0.32 6.9E-06 41.8 2.0 88 148-235 31-147 (160)
5 PRK05932 RNA polymerase factor 84.5 2.4 5.2E-05 41.6 6.1 89 148-236 325-442 (455)
6 COG1508 RpoN DNA-directed RNA 83.5 3.4 7.4E-05 41.3 6.8 99 138-236 301-430 (444)
7 PLN02777 photosystem I P subun 82.6 0.99 2.1E-05 40.2 2.4 27 1-27 1-41 (167)
8 PRK12469 RNA polymerase factor 79.0 5.3 0.00011 39.9 6.4 89 148-236 351-468 (481)
9 PF03874 RNA_pol_Rpb4: RNA pol 77.4 7.1 0.00015 30.4 5.4 56 171-226 27-83 (117)
10 smart00657 RPOL4c DNA-directed 76.3 7.4 0.00016 31.4 5.4 44 181-224 35-79 (118)
11 PF14297 DUF4373: Domain of un 76.3 13 0.00029 28.1 6.5 70 156-226 1-70 (87)
12 smart00422 HTH_MERR helix_turn 72.6 18 0.00039 25.0 6.0 54 169-224 3-68 (70)
13 PF06570 DUF1129: Protein of u 71.5 6.4 0.00014 34.0 4.3 49 198-254 6-56 (206)
14 PLN02196 abscisic acid 8'-hydr 70.2 15 0.00032 34.2 6.6 141 93-253 31-188 (463)
15 cd04780 HTH_MerR-like_sg5 Heli 70.1 16 0.00034 28.5 5.7 56 169-225 3-70 (95)
16 COG4915 XpaC 5-bromo-4-chloroi 68.3 18 0.0004 33.3 6.6 53 171-232 58-115 (204)
17 PF06798 PrkA: PrkA serine pro 65.6 44 0.00095 30.7 8.5 72 164-235 148-242 (254)
18 TIGR01359 UMP_CMP_kin_fam UMP- 64.7 23 0.0005 28.4 5.9 58 164-227 10-71 (183)
19 PF01402 RHH_1: Ribbon-helix-h 64.3 14 0.0003 23.7 3.8 27 167-193 12-38 (39)
20 TIGR00865 bcl-2 Apoptosis regu 63.9 11 0.00023 34.2 4.2 64 178-241 3-89 (213)
21 PRK10072 putative transcriptio 63.6 6 0.00013 31.6 2.3 52 201-253 34-88 (96)
22 cd01104 HTH_MlrA-CarA Helix-Tu 63.2 30 0.00066 23.9 5.6 54 169-223 3-67 (68)
23 KOG2351 RNA polymerase II, fou 63.0 18 0.00039 31.6 5.2 37 179-215 49-86 (134)
24 TIGR01128 holA DNA polymerase 62.7 28 0.0006 30.0 6.4 65 146-211 113-180 (302)
25 PF02847 MA3: MA3 domain; Int 62.3 8.9 0.00019 29.0 3.0 78 151-230 7-85 (113)
26 PRK06585 holA DNA polymerase I 61.8 32 0.0007 30.9 6.9 62 146-207 144-208 (343)
27 PRK00440 rfc replication facto 61.3 1E+02 0.0022 26.7 9.5 73 146-226 163-238 (319)
28 PRK05574 holA DNA polymerase I 60.5 33 0.00072 30.1 6.6 64 146-210 148-214 (340)
29 PF11166 DUF2951: Protein of u 60.4 5.9 0.00013 32.9 1.8 21 108-129 75-95 (98)
30 PF09840 DUF2067: Uncharacteri 60.2 22 0.00048 31.6 5.5 73 176-254 71-157 (190)
31 cd04765 HTH_MlrA-like_sg2 Heli 59.3 69 0.0015 25.1 7.5 55 170-225 4-70 (99)
32 cd04764 HTH_MlrA-like_sg1 Heli 59.1 31 0.00067 24.2 5.1 53 170-224 4-67 (67)
33 PHA01748 hypothetical protein 59.1 12 0.00025 27.5 3.0 29 168-196 16-44 (60)
34 smart00845 GatB_Yqey GatB doma 58.9 27 0.00058 28.7 5.4 46 196-241 38-89 (147)
35 COG4174 ABC-type uncharacteriz 58.8 13 0.00028 36.4 4.1 50 160-209 76-131 (364)
36 PRK07452 DNA polymerase III su 57.6 41 0.00088 30.0 6.7 59 149-207 135-197 (326)
37 PF07568 HisKA_2: Histidine ki 57.3 18 0.00038 27.0 3.8 33 198-231 9-41 (76)
38 smart00352 POU Found in Pit-Oc 57.3 13 0.00027 29.4 3.1 24 201-224 12-35 (75)
39 PRK12402 replication factor C 56.8 64 0.0014 28.2 7.7 76 147-227 187-263 (337)
40 smart00544 MA3 Domain in DAP-5 56.4 39 0.00085 25.7 5.6 84 151-240 7-91 (113)
41 KOG0488 Transcription factor B 56.2 13 0.00027 35.2 3.4 48 160-225 175-222 (309)
42 KOG2499 Beta-N-acetylhexosamin 55.1 14 0.0003 38.2 3.7 51 142-192 306-373 (542)
43 PF02417 Chromate_transp: Chro 54.4 8.8 0.00019 32.1 1.9 65 69-136 29-104 (169)
44 cd00056 ENDO3c endonuclease II 54.0 41 0.0009 26.9 5.6 69 158-242 11-79 (158)
45 smart00265 BH4 BH4 Bcl-2 homol 53.6 14 0.0003 24.4 2.3 23 177-199 2-24 (27)
46 cd04411 Ribosomal_P1_P2_L12p R 53.3 5.8 0.00013 32.3 0.7 10 68-77 93-102 (105)
47 PF00428 Ribosomal_60s: 60s Ac 53.3 1 2.2E-05 34.6 -3.5 7 69-75 77-83 (88)
48 COG2137 OraA Uncharacterized p 52.8 38 0.00082 29.8 5.6 59 182-242 34-93 (174)
49 PF08542 Rep_fac_C: Replicatio 52.8 41 0.00088 24.6 5.0 39 166-206 24-62 (89)
50 cd00592 HTH_MerR-like Helix-Tu 51.8 64 0.0014 24.2 6.0 55 169-225 3-68 (100)
51 PF11836 DUF3356: Protein of u 50.8 42 0.00091 26.9 5.2 67 163-242 17-87 (101)
52 PF02885 Glycos_trans_3N: Glyc 49.0 47 0.001 24.0 4.8 27 196-222 31-57 (66)
53 PF01381 HTH_3: Helix-turn-hel 48.5 14 0.0003 24.6 1.8 27 206-233 2-28 (55)
54 PRK03987 translation initiatio 48.4 65 0.0014 29.7 6.7 63 166-229 101-167 (262)
55 PF13560 HTH_31: Helix-turn-he 47.7 56 0.0012 22.8 4.9 53 168-221 5-63 (64)
56 PRK06645 DNA polymerase III su 47.3 1E+02 0.0022 31.0 8.3 61 146-206 189-253 (507)
57 TIGR00270 conserved hypothetic 47.0 39 0.00084 29.0 4.7 79 132-219 49-128 (154)
58 PRK00117 recX recombination re 46.5 50 0.0011 26.9 5.1 65 168-240 17-82 (157)
59 PF15176 LRR19-TM: Leucine-ric 46.0 21 0.00047 29.8 2.9 49 94-142 5-57 (102)
60 PRK11448 hsdR type I restricti 45.9 86 0.0019 34.5 8.1 78 141-225 966-1052(1123)
61 PF06972 DUF1296: Protein of u 45.8 17 0.00036 28.0 2.1 40 207-257 11-51 (60)
62 PRK13344 spxA transcriptional 45.4 86 0.0019 25.8 6.3 80 161-240 34-131 (132)
63 PRK14038 ADP-dependent glucoki 44.5 22 0.00048 35.7 3.3 104 131-234 188-315 (453)
64 PF12446 DUF3682: Protein of u 44.5 11 0.00025 32.7 1.1 16 61-76 93-108 (133)
65 PF08069 Ribosomal_S13_N: Ribo 44.2 23 0.0005 26.9 2.6 28 197-225 28-56 (60)
66 PRK06266 transcription initiat 44.2 35 0.00077 29.7 4.1 44 178-224 4-47 (178)
67 KOG1577 Aldo/keto reductase fa 43.1 70 0.0015 30.7 6.2 64 162-229 218-288 (300)
68 cd00086 homeodomain Homeodomai 42.9 51 0.0011 21.8 3.9 38 145-183 7-44 (59)
69 PRK14955 DNA polymerase III su 42.9 1.7E+02 0.0038 27.6 8.7 61 146-206 188-254 (397)
70 PF00046 Homeobox: Homeobox do 42.1 47 0.001 22.4 3.7 40 143-183 5-44 (57)
71 PHA02902 putative IMV membrane 41.8 22 0.00048 28.1 2.2 54 109-174 8-64 (70)
72 PF02180 BH4: Bcl-2 homology r 41.5 12 0.00027 24.7 0.7 23 178-200 3-25 (27)
73 PHA01976 helix-turn-helix prot 41.0 19 0.00042 24.9 1.7 30 203-233 5-34 (67)
74 TIGR02051 MerR Hg(II)-responsi 40.6 98 0.0021 24.8 5.8 55 169-224 2-67 (124)
75 PRK10026 arsenate reductase; P 39.3 43 0.00093 28.4 3.8 80 161-241 36-135 (141)
76 PF02797 Chal_sti_synt_C: Chal 39.2 22 0.00048 30.1 2.1 35 198-237 66-100 (151)
77 PTZ00373 60S Acidic ribosomal 38.8 11 0.00024 31.3 0.3 9 69-77 100-108 (112)
78 PRK07668 hypothetical protein; 38.8 45 0.00097 31.1 4.1 48 198-253 6-56 (254)
79 PHA00739 V3 structural protein 38.7 21 0.00046 29.4 1.8 35 88-122 42-79 (92)
80 PLN00138 large subunit ribosom 38.6 11 0.00024 31.2 0.2 12 66-77 98-109 (113)
81 PHA02591 hypothetical protein; 38.3 26 0.00057 28.5 2.2 36 198-234 44-79 (83)
82 PF08006 DUF1700: Protein of u 38.3 36 0.00078 28.5 3.2 30 207-236 34-66 (181)
83 PTZ00240 60S ribosomal protein 38.0 10 0.00022 36.3 -0.1 12 66-77 308-319 (323)
84 PRK14970 DNA polymerase III su 37.9 2.1E+02 0.0045 26.1 8.2 59 147-207 170-231 (367)
85 PTZ00072 40S ribosomal protein 37.8 40 0.00086 29.8 3.4 40 196-235 24-76 (148)
86 PRK09726 antitoxin HipB; Provi 37.6 42 0.0009 25.3 3.1 38 195-233 6-44 (88)
87 TIGR01360 aden_kin_iso1 adenyl 37.6 1.2E+02 0.0026 24.1 5.9 67 169-241 20-89 (188)
88 PRK14954 DNA polymerase III su 37.4 2E+02 0.0044 29.7 8.9 60 147-206 189-254 (620)
89 PF06595 BDV_P24: Borna diseas 37.4 24 0.00051 32.3 2.1 81 131-234 25-108 (201)
90 PRK00117 recX recombination re 37.2 2.3E+02 0.0049 23.1 7.6 110 130-251 23-139 (157)
91 PRK08561 rps15p 30S ribosomal 37.1 50 0.0011 29.2 3.9 40 196-235 27-79 (151)
92 COG2059 ChrA Chromate transpor 37.0 30 0.00064 31.0 2.6 63 68-134 33-107 (195)
93 PF00248 Aldo_ket_red: Aldo/ke 36.9 62 0.0013 27.7 4.4 55 164-222 216-278 (283)
94 PRK09111 DNA polymerase III su 36.4 1.7E+02 0.0036 30.1 8.0 60 146-207 193-255 (598)
95 PF06281 DUF1035: Protein of u 36.2 28 0.0006 27.7 2.0 42 89-130 24-68 (73)
96 KOG3449 60S acidic ribosomal p 35.9 19 0.00041 30.6 1.1 9 69-77 100-108 (112)
97 PF00620 RhoGAP: RhoGAP domain 35.7 81 0.0018 24.5 4.6 57 145-207 26-82 (151)
98 KOG4718 Non-SMC (structural ma 35.7 76 0.0016 30.0 5.1 72 171-242 86-164 (235)
99 cd04770 HTH_HMRTR Helix-Turn-H 35.7 1.9E+02 0.0041 22.7 6.7 8 175-182 55-62 (123)
100 KOG2286 Exocyst complex subuni 35.6 66 0.0014 34.0 5.1 94 118-236 481-582 (667)
101 PTZ00135 60S acidic ribosomal 35.5 11 0.00025 35.4 -0.2 11 66-76 295-305 (310)
102 cd04765 HTH_MlrA-like_sg2 Heli 35.2 50 0.0011 25.9 3.3 54 178-231 39-93 (99)
103 PF08461 HTH_12: Ribonuclease 34.7 89 0.0019 23.1 4.4 43 155-198 5-48 (66)
104 PRK04195 replication factor C 34.6 2.1E+02 0.0046 27.7 8.0 90 108-223 304-403 (482)
105 PF13443 HTH_26: Cro/C1-type H 34.6 1.2E+02 0.0026 20.7 4.8 44 170-219 14-57 (63)
106 cd04784 HTH_CadR-PbrR Helix-Tu 34.3 1.9E+02 0.0041 23.0 6.6 10 174-183 54-63 (127)
107 PRK06361 hypothetical protein; 34.1 55 0.0012 27.6 3.6 40 196-235 173-212 (212)
108 smart00229 RasGEFN Guanine nuc 33.9 2.2E+02 0.0048 21.9 6.9 95 118-229 25-125 (127)
109 cd05833 Ribosomal_P2 Ribosomal 33.6 17 0.00037 29.9 0.5 7 71-77 99-105 (109)
110 PF03874 RNA_pol_Rpb4: RNA pol 33.5 2.2E+02 0.0049 22.1 6.7 83 139-228 30-115 (117)
111 COG4858 Uncharacterized membra 33.4 72 0.0016 29.9 4.5 27 211-237 33-61 (226)
112 KOG2629 Peroxisomal membrane a 33.2 1.8E+02 0.0039 28.4 7.2 106 100-226 77-184 (300)
113 PRK03892 ribonuclease P protei 33.0 98 0.0021 28.8 5.3 65 169-233 137-215 (216)
114 PF12324 HTH_15: Helix-turn-he 32.9 71 0.0015 25.4 3.8 54 179-238 21-74 (77)
115 TIGR02384 RelB_DinJ addiction 32.9 2.3E+02 0.005 21.9 6.7 33 168-200 16-50 (83)
116 TIGR01856 hisJ_fam histidinol 32.7 1.5E+02 0.0032 26.2 6.2 79 165-243 121-207 (253)
117 PF13744 HTH_37: Helix-turn-he 32.6 49 0.0011 24.6 2.8 23 202-224 20-42 (80)
118 PF05598 DUF772: Transposase d 32.5 62 0.0013 23.1 3.2 31 196-226 4-35 (77)
119 COG5590 Uncharacterized conser 32.5 1.7E+02 0.0038 27.6 6.8 52 145-198 28-95 (229)
120 cd08315 Death_TRAILR_DR4_DR5 D 32.4 1.2E+02 0.0027 23.9 5.1 74 151-229 4-80 (96)
121 PRK13765 ATP-dependent proteas 32.2 1.1E+02 0.0024 31.7 6.1 63 179-242 315-391 (637)
122 PHA03211 serine/threonine kina 32.2 20 0.00044 34.4 0.8 36 64-99 92-127 (461)
123 PRK11172 dkgB 2,5-diketo-D-glu 32.2 1.7E+02 0.0036 25.8 6.5 58 165-227 188-251 (267)
124 PF04695 Pex14_N: Peroxisomal 31.9 1.3E+02 0.0029 24.8 5.5 50 180-230 2-51 (136)
125 PF08519 RFC1: Replication fac 31.7 20 0.00043 30.5 0.6 69 179-250 77-150 (155)
126 PRK13890 conjugal transfer pro 31.3 1.6E+02 0.0036 23.8 5.8 42 171-219 23-64 (120)
127 PLN03244 alpha-amylase; Provis 31.1 28 0.00061 37.8 1.7 20 5-24 1-20 (872)
128 cd01108 HTH_CueR Helix-Turn-He 31.0 2.5E+02 0.0054 22.5 6.8 9 175-183 55-63 (127)
129 cd07321 Extradiol_Dioxygenase_ 31.0 45 0.00098 25.5 2.4 55 185-239 6-60 (77)
130 PF07395 Mig-14: Mig-14; Inte 30.8 79 0.0017 29.9 4.4 100 123-258 98-200 (264)
131 PRK14958 DNA polymerase III su 30.8 2.5E+02 0.0054 28.1 8.0 75 146-227 180-257 (509)
132 PF09279 EF-hand_like: Phospho 30.5 85 0.0018 22.8 3.7 68 181-252 3-71 (83)
133 PF10771 DUF2582: Protein of u 30.4 62 0.0014 24.6 3.0 34 187-226 12-46 (65)
134 cd01310 TatD_DNAse TatD like p 30.4 82 0.0018 26.0 4.0 33 199-231 217-250 (251)
135 PF09524 Phg_2220_C: Conserved 30.4 1.3E+02 0.0029 23.4 4.9 54 170-224 3-59 (74)
136 PF13154 DUF3991: Protein of u 30.1 31 0.00067 25.7 1.4 19 189-207 1-19 (77)
137 cd00073 H15 linker histone 1 a 30.0 1.4E+02 0.003 22.9 4.9 46 146-193 8-53 (88)
138 PRK14951 DNA polymerase III su 30.0 3.3E+02 0.0072 28.3 9.0 59 146-206 185-246 (618)
139 PRK11565 dkgA 2,5-diketo-D-glu 29.9 1.8E+02 0.004 25.8 6.4 55 164-222 197-257 (275)
140 PF12651 RHH_3: Ribbon-helix-h 29.8 83 0.0018 21.8 3.4 28 167-194 15-42 (44)
141 PF04510 DUF577: Family of unk 29.7 1.2E+02 0.0026 27.4 5.1 84 92-194 89-174 (174)
142 cd01836 FeeA_FeeB_like SGNH_hy 29.0 67 0.0015 25.7 3.2 39 218-256 133-173 (191)
143 TIGR03880 KaiC_arch_3 KaiC dom 28.9 2.4E+02 0.0052 23.7 6.6 60 182-242 93-152 (224)
144 cd01279 HTH_HspR-like Helix-Tu 28.7 1.8E+02 0.0038 22.6 5.4 55 169-224 4-69 (98)
145 PF08708 PriCT_1: Primase C te 28.5 1.6E+02 0.0035 21.1 4.8 22 211-232 50-71 (71)
146 cd04785 HTH_CadR-PbrR-like Hel 28.4 2.8E+02 0.006 22.3 6.6 14 194-207 55-68 (126)
147 PF01026 TatD_DNase: TatD rela 28.3 89 0.0019 27.3 4.1 36 197-232 219-255 (255)
148 PF02637 GatB_Yqey: GatB domai 28.3 2.8E+02 0.006 22.6 6.7 45 195-239 38-88 (148)
149 PF02631 RecX: RecX family; I 28.2 1.1E+02 0.0023 24.0 4.1 42 185-234 45-86 (121)
150 cd04773 HTH_TioE_rpt2 Second H 28.0 2.1E+02 0.0045 22.5 5.7 55 170-225 4-69 (108)
151 PF11169 DUF2956: Protein of u 27.8 46 0.00099 28.0 2.1 22 96-118 75-96 (103)
152 COG0283 Cmk Cytidylate kinase 27.7 76 0.0016 29.5 3.7 118 92-242 5-128 (222)
153 PRK13848 conjugal transfer pro 27.3 72 0.0016 26.7 3.1 31 206-236 33-66 (98)
154 TIGR02044 CueR Cu(I)-responsiv 27.1 3E+02 0.0065 22.0 6.6 9 175-183 55-63 (127)
155 COG2761 FrnE Predicted dithiol 27.0 1.1E+02 0.0024 28.3 4.6 56 145-205 119-174 (225)
156 PF10746 Phage_holin_6: Phage 26.8 40 0.00087 26.3 1.5 46 87-132 4-60 (66)
157 cd04773 HTH_TioE_rpt2 Second H 26.8 2.9E+02 0.0063 21.7 6.4 52 178-230 39-90 (108)
158 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.8 3.2E+02 0.0068 22.1 6.7 9 175-183 55-63 (127)
159 PRK11477 carbohydrate diacid t 26.6 78 0.0017 29.2 3.6 36 144-179 318-365 (385)
160 COG2704 DcuB Anaerobic C4-dica 26.5 47 0.001 33.6 2.3 38 68-123 311-348 (436)
161 PF02459 Adeno_terminal: Adeno 26.1 33 0.00071 35.6 1.1 21 65-85 318-338 (548)
162 cd04776 HTH_GnyR Helix-Turn-He 25.9 2.7E+02 0.0057 22.4 6.1 32 178-209 37-68 (118)
163 PF13565 HTH_32: Homeodomain-l 25.8 1.8E+02 0.004 20.5 4.7 40 184-223 35-77 (77)
164 cd03034 ArsC_ArsC Arsenate Red 25.8 1.5E+02 0.0033 23.2 4.6 26 161-186 33-58 (112)
165 PF12335 SBF2: Myotubularin pr 25.8 53 0.0011 30.0 2.3 69 166-236 47-121 (225)
166 PRK14964 DNA polymerase III su 25.7 4.1E+02 0.0089 26.9 8.6 59 146-206 177-238 (491)
167 PF10389 CoatB: Bacteriophage 25.7 55 0.0012 23.9 1.9 24 109-132 22-45 (46)
168 PF02954 HTH_8: Bacterial regu 25.6 81 0.0018 21.0 2.7 28 179-206 1-28 (42)
169 PRK01905 DNA-binding protein F 25.4 2E+02 0.0043 21.5 5.0 53 148-207 9-61 (77)
170 COG4860 Uncharacterized protei 25.4 96 0.0021 28.0 3.8 40 202-242 96-135 (170)
171 PRK00056 mtgA monofunctional b 25.3 4.7E+02 0.01 24.2 8.3 57 193-254 127-183 (236)
172 PF07261 DnaB_2: Replication i 25.2 64 0.0014 22.8 2.2 59 169-227 2-61 (77)
173 smart00422 HTH_MERR helix_turn 25.2 1.2E+02 0.0025 20.9 3.5 32 177-208 38-69 (70)
174 PRK14959 DNA polymerase III su 25.1 4.4E+02 0.0096 27.7 8.9 58 147-206 181-241 (624)
175 COG0599 Uncharacterized homolo 25.0 57 0.0012 26.0 2.1 21 206-226 75-97 (124)
176 cd08315 Death_TRAILR_DR4_DR5 D 25.0 64 0.0014 25.5 2.4 41 180-225 2-42 (96)
177 PRK11677 hypothetical protein; 24.9 59 0.0013 27.8 2.3 22 106-127 1-22 (134)
178 cd08316 Death_FAS_TNFRSF6 Deat 24.8 49 0.0011 26.6 1.7 33 152-184 6-38 (97)
179 PRK13749 transcriptional regul 24.7 1.1E+02 0.0024 25.4 3.8 56 169-225 6-72 (121)
180 PRK00430 fis global DNA-bindin 24.7 2.7E+02 0.0058 22.1 5.8 52 148-206 27-78 (95)
181 PF10551 MULE: MULE transposas 24.6 69 0.0015 23.1 2.3 27 235-263 58-88 (93)
182 cd01049 RNRR2 Ribonucleotide R 24.6 4.9E+02 0.011 23.0 9.9 138 73-235 118-267 (288)
183 PF02631 RecX: RecX family; I 24.4 1.1E+02 0.0024 23.9 3.6 37 185-224 31-67 (121)
184 TIGR02397 dnaX_nterm DNA polym 24.3 5E+02 0.011 23.0 9.1 59 146-206 178-239 (355)
185 KOG4129 Exopolyphosphatases an 24.3 1E+02 0.0023 30.8 4.1 95 77-188 134-244 (377)
186 PF13411 MerR_1: MerR HTH fami 24.1 64 0.0014 22.3 2.0 55 169-225 3-68 (69)
187 PRK09358 adenosine deaminase; 23.9 4.9E+02 0.011 23.6 8.1 23 213-235 111-133 (340)
188 TIGR00133 gatB glutamyl-tRNA(G 23.9 2.9E+02 0.0062 28.0 7.1 46 195-240 367-418 (478)
189 PF03147 FDX-ACB: Ferredoxin-f 23.7 77 0.0017 24.1 2.5 24 213-236 68-91 (94)
190 cd03025 DsbA_FrnE_like DsbA fa 23.6 1.5E+02 0.0033 23.7 4.3 37 149-185 107-144 (193)
191 PF13934 ELYS: Nuclear pore co 23.4 4.2E+02 0.0092 23.5 7.4 103 94-218 99-204 (226)
192 PF07766 LETM1: LETM1-like pro 23.4 1.2E+02 0.0026 27.7 4.1 121 96-227 69-233 (268)
193 PF12844 HTH_19: Helix-turn-he 23.4 1.6E+02 0.0036 20.0 3.9 33 185-219 26-58 (64)
194 PF09677 TrbI_Ftype: Type-F co 23.3 1.8E+02 0.0038 24.0 4.7 41 149-189 38-79 (111)
195 PRK14530 adenylate kinase; Pro 23.3 1.3E+02 0.0027 25.5 4.0 57 168-226 19-78 (215)
196 TIGR03290 CoB_CoM_SS_C CoB--Co 23.2 1.8E+02 0.0039 23.7 4.7 47 160-216 96-142 (144)
197 PF01978 TrmB: Sugar-specific 23.0 1.1E+02 0.0025 21.5 3.1 47 175-229 3-49 (68)
198 cd03022 DsbA_HCCA_Iso DsbA fam 23.0 1.7E+02 0.0037 23.4 4.5 36 148-183 105-140 (192)
199 cd04774 HTH_YfmP Helix-Turn-He 22.9 2.3E+02 0.005 22.0 5.1 34 178-211 38-72 (96)
200 PF01323 DSBA: DSBA-like thior 22.8 2.1E+02 0.0045 22.8 4.9 79 148-257 105-188 (193)
201 PF07308 DUF1456: Protein of u 22.8 83 0.0018 23.9 2.5 38 182-224 3-40 (68)
202 PRK13481 glycosyltransferase; 22.8 1.6E+02 0.0034 27.3 4.8 55 193-253 111-166 (232)
203 KOG1869 Splicing coactivator S 22.7 1.2E+02 0.0026 30.8 4.2 52 169-220 73-145 (425)
204 cd08801 Death_UNC5D Death doma 22.6 2.3E+02 0.0049 23.8 5.2 67 149-228 9-75 (98)
205 PF02581 TMP-TENI: Thiamine mo 22.6 20 0.00044 29.8 -0.8 69 203-273 26-104 (180)
206 PF00406 ADK: Adenylate kinase 22.6 2.2E+02 0.0048 22.4 5.0 64 170-240 14-80 (151)
207 PRK08456 flagellar motor prote 22.6 3.8E+02 0.0082 24.5 7.1 54 148-207 76-129 (257)
208 PRK14961 DNA polymerase III su 22.5 6.4E+02 0.014 23.5 9.0 57 148-206 182-241 (363)
209 TIGR00008 infA translation ini 22.4 26 0.00057 27.0 -0.2 19 83-101 2-20 (68)
210 PRK06305 DNA polymerase III su 22.4 5.1E+02 0.011 25.4 8.4 59 146-206 182-243 (451)
211 PRK08691 DNA polymerase III su 22.3 4.7E+02 0.01 28.1 8.6 59 147-207 181-242 (709)
212 PF07638 Sigma70_ECF: ECF sigm 22.2 84 0.0018 26.3 2.7 35 198-233 136-170 (185)
213 COG2905 Predicted signal-trans 22.2 89 0.0019 33.0 3.3 59 201-268 295-353 (610)
214 PF00690 Cation_ATPase_N: Cati 22.2 58 0.0013 23.2 1.5 34 198-239 5-38 (69)
215 PF03162 Y_phosphatase2: Tyros 22.2 24 0.00052 30.0 -0.5 30 161-193 104-133 (164)
216 PRK00440 rfc replication facto 22.2 2.4E+02 0.0053 24.3 5.6 35 171-206 252-286 (319)
217 PF02796 HTH_7: Helix-turn-hel 22.2 64 0.0014 21.8 1.6 29 195-224 4-32 (45)
218 PF09548 Spore_III_AB: Stage I 22.1 4.9E+02 0.011 22.0 7.7 52 170-221 75-126 (170)
219 PRK08451 DNA polymerase III su 22.0 4.6E+02 0.0099 26.9 8.2 58 146-205 178-238 (535)
220 PRK12559 transcriptional regul 22.0 2.7E+02 0.0058 22.9 5.5 64 161-224 34-115 (131)
221 PRK00767 transcriptional regul 21.8 4.1E+02 0.009 21.1 7.4 51 179-230 82-132 (197)
222 PRK05477 gatB aspartyl/glutamy 21.7 1.9E+02 0.0042 29.2 5.5 47 193-239 362-414 (474)
223 TIGR01167 LPXTG_anchor LPXTG-m 21.7 96 0.0021 19.4 2.3 21 99-119 3-23 (34)
224 TIGR03070 couple_hipB transcri 21.7 1.3E+02 0.0028 19.5 3.0 21 204-224 6-26 (58)
225 COG0015 PurB Adenylosuccinate 21.6 3.9E+02 0.0085 27.0 7.5 82 161-242 54-144 (438)
226 PRK12442 translation initiatio 21.5 28 0.00061 28.2 -0.2 18 83-100 4-21 (87)
227 smart00389 HOX Homeodomain. DN 21.5 2E+02 0.0043 18.9 3.9 37 146-183 8-44 (56)
228 PRK15043 transcriptional regul 21.4 2.1E+02 0.0045 26.6 5.2 55 170-225 7-72 (243)
229 PF01369 Sec7: Sec7 domain; I 21.3 1.7E+02 0.0036 25.1 4.4 38 195-234 34-74 (190)
230 PRK09885 putative toxin YafO; 21.3 65 0.0014 27.9 1.9 30 186-216 8-37 (132)
231 PF10540 Membr_traf_MHD: Munc1 21.2 64 0.0014 26.7 1.8 23 147-169 88-110 (137)
232 cd07922 CarBa CarBa is the A s 21.2 84 0.0018 24.9 2.4 46 185-230 7-52 (81)
233 COG2212 MnhF Multisubunit Na+/ 21.2 73 0.0016 25.8 2.1 39 106-148 3-41 (89)
234 PRK14952 DNA polymerase III su 21.1 5.2E+02 0.011 26.6 8.4 60 146-206 179-241 (584)
235 KOG0774 Transcription factor P 21.1 1.2E+02 0.0027 29.6 3.9 82 130-216 183-270 (334)
236 PF11377 DUF3180: Protein of u 21.1 50 0.0011 27.7 1.1 38 105-144 28-65 (138)
237 PF07820 TraC: TraC-like prote 21.1 1.1E+02 0.0023 25.3 3.0 33 205-237 31-66 (92)
238 PLN02200 adenylate kinase fami 21.1 3.8E+02 0.0082 23.7 6.7 93 159-259 49-152 (234)
239 cd04763 HTH_MlrA-like Helix-Tu 20.9 1.5E+02 0.0032 20.9 3.3 53 170-224 4-68 (68)
240 PF09162 Tap-RNA_bind: Tap, RN 20.9 36 0.00077 27.4 0.2 23 214-236 51-73 (88)
241 PRK09514 zntR zinc-responsive 20.7 3.7E+02 0.0079 22.2 6.1 16 192-207 54-69 (140)
242 PF01726 LexA_DNA_bind: LexA D 20.6 2.2E+02 0.0047 21.1 4.3 41 147-190 9-49 (65)
243 PF04801 Sin_N: Sin-like prote 20.6 1.3E+02 0.0027 28.8 3.8 44 181-229 335-378 (421)
244 cd07212 Pat_PNPLA9 Patatin-lik 20.5 3.1E+02 0.0068 25.4 6.2 51 163-226 38-88 (312)
245 cd05197 GH4_glycoside_hydrolas 20.5 1.2E+02 0.0026 29.6 3.7 57 197-254 12-78 (425)
246 cd05029 S-100A6 S-100A6: S-100 20.5 2.9E+02 0.0063 21.1 5.1 44 180-226 12-60 (88)
247 PRK14963 DNA polymerase III su 20.4 5.2E+02 0.011 25.9 8.1 58 146-206 177-237 (504)
248 PRK07764 DNA polymerase III su 20.4 5.4E+02 0.012 27.7 8.6 60 146-206 181-243 (824)
249 PRK00464 nrdR transcriptional 20.4 2.9E+02 0.0063 24.0 5.6 61 193-254 57-122 (154)
250 PF14567 SUKH_5: SMI1-KNR4 cel 20.2 2.7E+02 0.0058 23.8 5.3 53 163-216 21-85 (132)
251 cd01105 HTH_GlnR-like Helix-Tu 20.2 1.6E+02 0.0035 22.3 3.7 31 194-225 37-70 (88)
252 PTZ00397 macrophage migration 20.2 62 0.0013 25.3 1.4 53 212-266 10-66 (116)
253 PF02936 COX4: Cytochrome c ox 20.2 56 0.0012 27.8 1.3 40 97-136 63-102 (142)
254 PRK05629 hypothetical protein; 20.1 5.2E+02 0.011 23.4 7.4 59 147-207 129-190 (318)
255 PTZ00234 variable surface prot 20.0 54 0.0012 32.6 1.3 34 112-145 369-404 (433)
256 PRK04028 glutamyl-tRNA(Gln) am 20.0 1.5E+02 0.0032 31.2 4.4 46 196-241 518-570 (630)
257 PF10408 Ufd2P_core: Ubiquitin 20.0 1.9E+02 0.0041 29.2 5.0 57 174-230 557-627 (629)
258 COG1140 NarY Nitrate reductase 20.0 2.7E+02 0.0059 28.8 6.1 64 148-227 386-449 (513)
259 PRK11235 bifunctional antitoxi 20.0 4E+02 0.0087 21.0 5.9 54 169-235 16-71 (80)
No 1
>KOG0154 consensus RNA-binding protein RBM5 and related proteins, contain G-patch and RRM domains [General function prediction only]
Probab=97.94 E-value=6.7e-07 Score=86.46 Aligned_cols=191 Identities=16% Similarity=0.069 Sum_probs=158.0
Q ss_pred hhhHHHHhcchhhHHhhhhhhhhccccccccCCCcCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcc
Q 023705 66 EVEVEVEEELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNK 145 (278)
Q Consensus 66 e~e~e~e~e~~wiqekaldlveftG~vtQAIPGPRVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNK 145 (278)
+.++..+++.+|+++++.+-++|+....|.+.+++...+-++|-++-.+++.|.+.+..++....+....|.+.+....=
T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~l~~d~~~s~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~i~q~~~~~~~~~ 314 (573)
T KOG0154|consen 235 ETDEYYEDPETSVYYDTDSGLYFNDASSQYLYGDDEQSDYFYAKLSPSLPEFGVPNALQKKKKKEKPKIAQVKTKDMEKW 314 (573)
T ss_pred cccCceecCCccceeeccccceeccccccccccCCCcceeeecccccccccccccHHHhhhcccccccchhhhhhhHHhh
Confidence 55666678899999999999999999999999999999999999999999999999999999999999999999888888
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhc--CCCcHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKAS--MLDDSQVAEIL 223 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas--~L~D~evaEiL 223 (278)
++++.+..|+|.-.. ...+.....++....|.....|..+|..|..+|+.++|+.+...+|.+... +|.+...+..-
T Consensus 315 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 393 (573)
T KOG0154|consen 315 AKYLSKEKDSYLLSS-TPAHEGVHTGVNTSKGAEPGPVKKEKKLYKKKEKFVNPELSKRGSHVSPSKNLKLIDVSTGLSD 393 (573)
T ss_pred hhhhhcccccccccc-cccceecccccccccccCchhhhhhccccccchhccCccccccccccCccccccccccccCCCc
Confidence 899998888876554 447888889999999999999999999999999999999999999998863 44444444444
Q ss_pred HHHHHhhh---hhcCccccccc-------hhhhhhcccCCccch
Q 023705 224 NEISRRFV---REKDEDALDEQ-------PPMQALFVFDPVHNI 257 (278)
Q Consensus 224 nE~srRiv---~~~G~vmmn~~-------~avqalf~~~~~~~~ 257 (278)
++.....- -+++..+..+- .++|.-|..-.+|+.
T Consensus 394 ~~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~s~~h~~ 437 (573)
T KOG0154|consen 394 SELEQEKSLKLVDKLKLMCLLCRRQFPSKGSLQKHLTPSDLHKE 437 (573)
T ss_pred hHhhhhhhhhccccchhhhhhhhccCCchHHHhhhcccccchhh
Confidence 44444444 33444444443 777888887777754
No 2
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.26 E-value=0.69 Score=42.73 Aligned_cols=79 Identities=18% Similarity=0.206 Sum_probs=63.5
Q ss_pred hhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhc-CCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCC
Q 023705 118 GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQK-GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKP 196 (278)
Q Consensus 118 G~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~-gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~ 196 (278)
||-++.-..|+.+-=|.-|-|=+--+.+-..-++.|.+|+.+ .-++-+..-.|--++.||||-+-||++|..=.|+|--
T Consensus 41 GIdLi~e~lk~~~ldna~R~~i~~k~s~Ym~ka~diekYLdqekEdgk~~eQ~KI~~NaTG~SY~~iF~e~~dd~l~~V~ 120 (247)
T KOG4509|consen 41 GIDLIAEALKGMKLDNADRCKIMAKFSDYMDKAADIEKYLDQEKEDGKTHEQIKIAANATGFSYARIFGECCDDRLREVH 120 (247)
T ss_pred hHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhccCcccHHHHHHHHHhhhhheee
Confidence 888888888887766666666666667777778889999985 5566677777778899999999999999998888753
No 3
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=88.36 E-value=1.6 Score=42.40 Aligned_cols=89 Identities=27% Similarity=0.483 Sum_probs=69.9
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHHhcC--------CCCChHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNE--------KPFNPDLVVNLI 206 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R----KYi---------rY~LnE--------r~F~pd~VaDLi 206 (278)
.||+.=.+||..|...+.+=.||.+..++|.+-.-|=| ||+ +|.... ...+.+.|-+.|
T Consensus 300 ~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I 379 (429)
T TIGR02395 300 AIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALI 379 (429)
T ss_pred HHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHH
Confidence 35555578999999999999999999999999998887 785 566542 236777776665
Q ss_pred HH-----HhhcCCCcHHHHHHHHH----HHHhhhhhcCc
Q 023705 207 QL-----RKASMLDDSQVAEILNE----ISRRFVREKDE 236 (278)
Q Consensus 207 ~L-----rkas~L~D~evaEiLnE----~srRiv~~~G~ 236 (278)
+- -+.--|||.+++++|.+ ||||-|-||=.
T Consensus 380 ~~lI~~E~~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe 418 (429)
T TIGR02395 380 KELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYRE 418 (429)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHhcCCCeehHHHHHHHH
Confidence 52 23456999999999985 89999999954
No 4
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=88.22 E-value=0.32 Score=41.79 Aligned_cols=88 Identities=27% Similarity=0.457 Sum_probs=20.8
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHHHH---------HhcCC-------CCChHHHHHHH-
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYIRY---------ALNEK-------PFNPDLVVNLI- 206 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R----KYirY---------~LnEr-------~F~pd~VaDLi- 206 (278)
+||+.=.+||..|...+.+=-++.+...+|++..-|=| ||+.. .+.-. .++.+.|-+.|
T Consensus 31 ~iv~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~ 110 (160)
T PF04552_consen 31 AIVERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIK 110 (160)
T ss_dssp ------------------------------------------------------S-----SS--SS-SS---TTH-HHHH
T ss_pred HHHHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHH
Confidence 56777788999888899999999999999999998877 88753 22211 13444454333
Q ss_pred ---HH-HhhcCCCcHHHHHHHH----HHHHhhhhhcC
Q 023705 207 ---QL-RKASMLDDSQVAEILN----EISRRFVREKD 235 (278)
Q Consensus 207 ---~L-rkas~L~D~evaEiLn----E~srRiv~~~G 235 (278)
+= -+.-.|||++++++|+ .+|||-|-||=
T Consensus 111 ~lI~~Ed~~~PlSD~~i~~~L~~~gi~isRRTVaKYR 147 (160)
T PF04552_consen 111 ELIEEEDKKKPLSDQEIAELLKEEGIKISRRTVAKYR 147 (160)
T ss_dssp HHHTTS-TTS---HHHHHHHHTTTTS---HHHHHHHH
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCCccHHHHHHHH
Confidence 32 2346899999999998 58999999984
No 5
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=84.53 E-value=2.4 Score=41.56 Aligned_cols=89 Identities=27% Similarity=0.505 Sum_probs=68.0
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHHhcCC-------CCChHHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNEK-------PFNPDLVVNLIQ 207 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R----KYi---------rY~LnEr-------~F~pd~VaDLi~ 207 (278)
.||+.=.+||..|...+.+=.||.+..+.|+.-.-|=| ||+ +|..... ..+.+.|-+.|+
T Consensus 325 ~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik 404 (455)
T PRK05932 325 CIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIK 404 (455)
T ss_pred HHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHH
Confidence 34555578999999999999999999999999998887 775 5555422 245566665554
Q ss_pred H-----HhhcCCCcHHHHHHHHH----HHHhhhhhcCc
Q 023705 208 L-----RKASMLDDSQVAEILNE----ISRRFVREKDE 236 (278)
Q Consensus 208 L-----rkas~L~D~evaEiLnE----~srRiv~~~G~ 236 (278)
- =+.--|||.+++++|.+ ||||-|-||=.
T Consensus 405 ~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe 442 (455)
T PRK05932 405 KLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYRE 442 (455)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCCeehHHHHHHHH
Confidence 2 12356999999999986 89999999954
No 6
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=83.55 E-value=3.4 Score=41.27 Aligned_cols=99 Identities=27% Similarity=0.474 Sum_probs=78.0
Q ss_pred hhhhhhcch-hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHH----hcCC----
Q 023705 138 KRKKLVNKN-AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYA----LNEK---- 195 (278)
Q Consensus 138 KRkR~VNKN-amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R----KYi---------rY~----LnEr---- 195 (278)
+|++++=|= .++|+-=++||..|..++.+=.||.+..+.|..-.-|-| ||+ +|. +...
T Consensus 301 qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~ 380 (444)
T COG1508 301 QREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGE 380 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCc
Confidence 455554442 367777789999999999999999999999999999988 775 443 3444
Q ss_pred CCChHHHHHHHH-----HHhhcCCCcHHHHHHHHH----HHHhhhhhcCc
Q 023705 196 PFNPDLVVNLIQ-----LRKASMLDDSQVAEILNE----ISRRFVREKDE 236 (278)
Q Consensus 196 ~F~pd~VaDLi~-----Lrkas~L~D~evaEiLnE----~srRiv~~~G~ 236 (278)
..+-+.|-++|. =++..-|||+.++++|-| +|||-|-||=.
T Consensus 381 ~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe 430 (444)
T COG1508 381 ASSTEAIKALIKKLIEAEDKKKPLSDSKIAELLKEKGIDVARRTVAKYRE 430 (444)
T ss_pred cccHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHcCCchhHHhHHHHHH
Confidence 578878877764 245568999999999997 79999999954
No 7
>PLN02777 photosystem I P subunit (PSI-P)
Probab=82.58 E-value=0.99 Score=40.18 Aligned_cols=27 Identities=41% Similarity=0.621 Sum_probs=16.4
Q ss_pred Ccccccccccc--------------ccccCCCCCCCCCCCC
Q 023705 1 MASLATSSFSS--------------LQFLPRPKIPQPPFSS 27 (278)
Q Consensus 1 ~~~~~~~~~~~--------------~q~~~~p~~p~~~~~~ 27 (278)
|++|.++|++| .|.+.-|.+|||+-.+
T Consensus 1 ~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~lp~lppp~~~~ 41 (167)
T PLN02777 1 MTPLSISSSSTLIDSKAPRSSAAASPQCVSLPTLPPPPVQS 41 (167)
T ss_pred CCccccccccccccCCCCCcCcccCCccccCCCCCCCCccc
Confidence 67777766655 4566666666654443
No 8
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=78.99 E-value=5.3 Score=39.88 Aligned_cols=89 Identities=26% Similarity=0.400 Sum_probs=68.7
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHHhcCC-------CCChHHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNEK-------PFNPDLVVNLIQ 207 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R----KYi---------rY~LnEr-------~F~pd~VaDLi~ 207 (278)
.+|+.=.+||..|...+.+=.||.+..+.|..-.-|=| ||+ +|...-. ..+.+.|-++|+
T Consensus 351 ~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik 430 (481)
T PRK12469 351 CIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIK 430 (481)
T ss_pred HHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHH
Confidence 34555568999999999999999999999999988877 784 5666422 245556666654
Q ss_pred H-----HhhcCCCcHHHHHHHHH----HHHhhhhhcCc
Q 023705 208 L-----RKASMLDDSQVAEILNE----ISRRFVREKDE 236 (278)
Q Consensus 208 L-----rkas~L~D~evaEiLnE----~srRiv~~~G~ 236 (278)
- -+.--|||.+++++|++ ||||-|-||=.
T Consensus 431 ~lI~~Ed~~kPLSD~~I~~~L~~~GI~IARRTVAKYRe 468 (481)
T PRK12469 431 EMIAAEQAGDPLSDVALAEMLAGRGVLIARRTVAKYRE 468 (481)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHhcCCCeechhHHHHHH
Confidence 3 22456999999999986 89999999955
No 9
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=77.37 E-value=7.1 Score=30.43 Aligned_cols=56 Identities=16% Similarity=0.166 Sum_probs=36.6
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcCCCCC-hHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023705 171 GLVQKTGFSMEDVLRKYIRYALNEKPFN-PDLVVNLIQLRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 171 ~L~~KTGFs~~EV~RKYirY~LnEr~F~-pd~VaDLi~Lrkas~L~D~evaEiLnE~ 226 (278)
...+.....+..+++|-+.|+-+=..+. ++.+..++..=+..||++.|+..|+|-.
T Consensus 27 ~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~ 83 (117)
T PF03874_consen 27 KNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQIINLR 83 (117)
T ss_dssp HHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHHHH-
T ss_pred ccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHhcCC
Confidence 4455566677777777777777766666 6777777776667777777777777643
No 10
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=76.27 E-value=7.4 Score=31.37 Aligned_cols=44 Identities=25% Similarity=0.379 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhcCCCC-ChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 181 EDVLRKYIRYALNEKPF-NPDLVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 181 ~EV~RKYirY~LnEr~F-~pd~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
.+|++|.+.|+-+=..| |++.+..+..+=+..+|++.|++-|.|
T Consensus 35 ~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~N 79 (118)
T smart00657 35 STVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQLGN 79 (118)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 45666666666444444 566666666655556666666655544
No 11
>PF14297 DUF4373: Domain of unknown function (DUF4373)
Probab=76.25 E-value=13 Score=28.07 Aligned_cols=70 Identities=17% Similarity=0.238 Sum_probs=55.1
Q ss_pred HHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023705 156 LFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 156 yFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~ 226 (278)
|||-.-+.++...++.|+++.|-.-.-|+-+=|.+.-.+.-+-...= ++..+-.-.+.|.+.|.+|++|.
T Consensus 1 YFp~dv~~~~D~ki~~l~~~~G~~G~~~y~~ll~~iy~~~~y~~~~~-~~~~~a~~~~~~~~~v~~II~~~ 70 (87)
T PF14297_consen 1 YFPLDVDFFSDPKIRRLMAEYGCEGYGIYWYLLEYIYKQGGYYLWWD-KLFLIARKLGVSEEYVEEIINEY 70 (87)
T ss_pred CcccccccccCHHHHHHHHHcCCchHHHHHHHHHHHHcCCCeEeeHH-HHHHHHHHHCcCHHHHHHHHHHh
Confidence 68888899999999999999999999999988888887776632211 14444455599999999999944
No 12
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=72.61 E-value=18 Score=25.04 Aligned_cols=54 Identities=20% Similarity=0.328 Sum_probs=38.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhc---------CCCCChHHHHHH---HHHHhhcCCCcHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYALN---------EKPFNPDLVVNL---IQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~Ln---------Er~F~pd~VaDL---i~Lrkas~L~D~evaEiLn 224 (278)
++++.+++|-+.. -+|+|.+.-+- .+-|+++.|..| ..||. .|++.++|+.+|+
T Consensus 3 ~~eva~~~gvs~~-tlr~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 3 IGEVAKLAGVSVR-TLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 4567788887764 45677665542 145888877654 56666 8999999999885
No 13
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=71.54 E-value=6.4 Score=33.96 Aligned_cols=49 Identities=24% Similarity=0.480 Sum_probs=38.0
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhh--hcCccccccchhhhhhcccCCc
Q 023705 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVR--EKDEDALDEQPPMQALFVFDPV 254 (278)
Q Consensus 198 ~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~--~~G~vmmn~~~avqalf~~~~~ 254 (278)
|+|.+.||-+-=++++++|+|+.|+|+|+-..+.+ +.|.- ..-+|| ||-
T Consensus 6 N~~y~~~l~~~L~~~~~~e~~~e~~L~eil~~LleaQk~G~t-------A~~lfG-~P~ 56 (206)
T PF06570_consen 6 NQEYIFDLRKYLRSSGVSEEEIEELLEEILPHLLEAQKKGKT-------ARQLFG-DPK 56 (206)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCCc-------HHHHcC-CHH
Confidence 67778887644488999999999999999999986 45643 345788 774
No 14
>PLN02196 abscisic acid 8'-hydroxylase
Probab=70.21 E-value=15 Score=34.22 Aligned_cols=141 Identities=14% Similarity=0.240 Sum_probs=69.3
Q ss_pred ccccCCCcCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHH---hhHHHHHhcCCCCCCch--
Q 023705 93 TQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVC---KTIDELFQKGGDAVNPP-- 167 (278)
Q Consensus 93 tQAIPGPRVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNKNamLv---kSLDeyFp~gRdal~~g-- 167 (278)
.+-+|||- |..++|+++-+...+ +-.....+.+..+||.+. =|-+..+++..++ +-+.+.|.++.+...+.
T Consensus 31 ~~~~~~Pp-gp~~~P~iG~~~~~~-~~~~~~~~~~~~~~yG~i--~~~~~~~~~~v~v~~p~~~~~vl~~~~~~~~~~~~ 106 (463)
T PLN02196 31 STKLPLPP-GTMGWPYVGETFQLY-SQDPNVFFASKQKRYGSV--FKTHVLGCPCVMISSPEAAKFVLVTKSHLFKPTFP 106 (463)
T ss_pred CCCCCCCC-CCCCCCccchHHHHH-hcCHHHHHHHHHHHhhhh--heeeecCCceEEEcCHHHHHHHHhCCCCcccccCc
Confidence 34567763 455688887543323 223445567788888642 2444556665554 23344554444433211
Q ss_pred -HHHHHHHHh--CCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccc--
Q 023705 168 -ALKGLVQKT--GFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQ-- 242 (278)
Q Consensus 168 -vLk~L~~KT--GFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~-- 242 (278)
..+.+..+. .++..|..++.=+.. + +.|+++.+..+ .+.++++++..+++.+.-.+|+.
T Consensus 107 ~~~~~~~g~~~l~~~~g~~w~~~Rk~l-~-~~f~~~~l~~~--------------~~~i~~~~~~~~~~~~~~~v~~~~~ 170 (463)
T PLN02196 107 ASKERMLGKQAIFFHQGDYHAKLRKLV-L-RAFMPDAIRNM--------------VPDIESIAQESLNSWEGTQINTYQE 170 (463)
T ss_pred hHHHHHcCcccccccCcHHHHHHHHHH-H-HhcChHHHHHH--------------HHHHHHHHHHHHHcCCCCeEEeHHH
Confidence 111111111 134455555443333 3 35776655443 23344444444444332223433
Q ss_pred -------hhhhhhcccCC
Q 023705 243 -------PPMQALFVFDP 253 (278)
Q Consensus 243 -------~avqalf~~~~ 253 (278)
.+.+++||.+-
T Consensus 171 ~~~~~~~v~~~~~fG~~~ 188 (463)
T PLN02196 171 MKTYTFNVALLSIFGKDE 188 (463)
T ss_pred HHHHHHHHHHHHHcCCCC
Confidence 56778999874
No 15
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=70.10 E-value=16 Score=28.49 Aligned_cols=56 Identities=27% Similarity=0.450 Sum_probs=44.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh---------cCCCCChHHHHHHHH---HHhhcCCCcHHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILNE 225 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~L---------nEr~F~pd~VaDLi~---Lrkas~L~D~evaEiLnE 225 (278)
+.++.+++|-+.. -+|-|.+.-| |.+-|+++.|..|-. ||+.+|++=+||+++|+.
T Consensus 3 I~eva~~~gvs~~-tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 3 MSELSKRSGVSVA-TIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4578889998876 5677777655 346799999988765 555689999999999987
No 16
>COG4915 XpaC 5-bromo-4-chloroindolyl phosphate hydrolysis protein [General function prediction only]
Probab=68.25 E-value=18 Score=33.27 Aligned_cols=53 Identities=32% Similarity=0.417 Sum_probs=40.7
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCc-----HHHHHHHHHHHHhhhh
Q 023705 171 GLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDD-----SQVAEILNEISRRFVR 232 (278)
Q Consensus 171 ~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D-----~evaEiLnE~srRiv~ 232 (278)
+-..++|-+-.|+ ||||=-|+| +=..++.|+|++-=.+ .|++++| ++|+|||.
T Consensus 58 ~~l~e~gLT~kdy--kyiR~nLee------arqki~~l~K~l~q~kslq~f~q~n~~l-~iskriy~ 115 (204)
T COG4915 58 ERLHEAGLTDKDY--KYIRENLEE------ARQKIKRLEKLLKQEKSLQVFEQVNGGL-EISKRIYK 115 (204)
T ss_pred HHHHHccCccchH--HHHHHhHHH------HHHHHHHHHHHHHhhhHHHHHHHHhhHH-HHHHHHHH
Confidence 3457889998887 899999986 5678888888876555 3677776 68999874
No 17
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=65.63 E-value=44 Score=30.72 Aligned_cols=72 Identities=17% Similarity=0.305 Sum_probs=50.5
Q ss_pred CCchHHHHHHHHhCCCh-------HHHHHHHHHHHhcCCCCChH---------------HHHHHHHHHh-hcCCCcHHHH
Q 023705 164 VNPPALKGLVQKTGFSM-------EDVLRKYIRYALNEKPFNPD---------------LVVNLIQLRK-ASMLDDSQVA 220 (278)
Q Consensus 164 l~~gvLk~L~~KTGFs~-------~EV~RKYirY~LnEr~F~pd---------------~VaDLi~Lrk-as~L~D~eva 220 (278)
.+..-|+.++.+-|.+- .||...|-+++-+-+.|+.+ .|.|++.+=. .+.-.|.+..
T Consensus 148 pdE~~mrsIEe~igi~~~~~~~FR~ei~~~~~~~~~~g~~~~~~~~e~Lr~~iEkkL~~d~~~~~~~~t~~~k~~d~e~~ 227 (254)
T PF06798_consen 148 PDERFMRSIEERIGISEEAKKDFRREIIKYISALAREGKKFDYTSYERLREAIEKKLFSDVKDLIKIITESSKTPDKEQQ 227 (254)
T ss_pred ccHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHcCCCCCChhhhHHHHHHHHHHHHHHHHHHHHhcchhccCCCHHHH
Confidence 34556788888777765 46777775555566888876 3555555444 4445688888
Q ss_pred HHHHHHHHhhhhhcC
Q 023705 221 EILNEISRRFVREKD 235 (278)
Q Consensus 221 EiLnE~srRiv~~~G 235 (278)
+-.++.-.|+.++||
T Consensus 228 ~~~~~~i~rL~~~~G 242 (254)
T PF06798_consen 228 RKIDEVIERLIKKYG 242 (254)
T ss_pred HHHHHHHHHHHHcCC
Confidence 888999999988888
No 18
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=64.71 E-value=23 Score=28.39 Aligned_cols=58 Identities=21% Similarity=0.357 Sum_probs=37.3
Q ss_pred CCchHH-HHHHHHhCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023705 164 VNPPAL-KGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (278)
Q Consensus 164 l~~gvL-k~L~~KTGF---s~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s 227 (278)
--++.+ +.|.++.|| |+.|++|++++ +..-....+.+++ ..+...+|+.+.+.|.+.-
T Consensus 10 sGKst~a~~la~~~~~~~is~~d~lr~~~~----~~~~~~~~~~~~~--~~g~~~~~~~~~~ll~~~~ 71 (183)
T TIGR01359 10 SGKGTQCAKIVENFGFTHLSAGDLLRAEIK----SGSENGELIESMI--KNGKIVPSEVTVKLLKNAI 71 (183)
T ss_pred CCHHHHHHHHHHHcCCeEEECChHHHHHHh----cCChHHHHHHHHH--HCCCcCCHHHHHHHHHHHH
Confidence 334455 788999998 68899999987 2222333455553 4556667776666666543
No 19
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=64.30 E-value=14 Score=23.69 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=23.6
Q ss_pred hHHHHHHHHhCCChHHHHHHHHHHHhc
Q 023705 167 PALKGLVQKTGFSMEDVLRKYIRYALN 193 (278)
Q Consensus 167 gvLk~L~~KTGFs~~EV~RKYirY~Ln 193 (278)
..|+.+..+.|-|..+++|..|+..++
T Consensus 12 ~~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 12 ERLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp HHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 467889999999999999999988764
No 20
>TIGR00865 bcl-2 Apoptosis regulator. in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
Probab=63.89 E-value=11 Score=34.16 Aligned_cols=64 Identities=22% Similarity=0.175 Sum_probs=45.2
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHH-----------HHHHHhh------------cCCCcHHHHHHHHHHHHhhhhhc
Q 023705 178 FSMEDVLRKYIRYALNEKPFNPDLVVN-----------LIQLRKA------------SMLDDSQVAEILNEISRRFVREK 234 (278)
Q Consensus 178 Fs~~EV~RKYirY~LnEr~F~pd~VaD-----------Li~Lrka------------s~L~D~evaEiLnE~srRiv~~~ 234 (278)
.|.-|++-|||-|.|.-+.+.++.-++ .++=|.. .+-..+++++.|+.++.-+=++|
T Consensus 3 ~~~r~~v~~~~~yklsq~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ps~v~~~Lr~igdEle~~~ 82 (213)
T TIGR00865 3 GSNRELVMKFISYKLSQRGGSWTAGEQIMKNGAPLLHGFIQHRAGPMTGETPSEGPPQDPPPSAVHQALRRAGDEFERRY 82 (213)
T ss_pred CchHHHHHHHHHHhhcccCCCCcchhhHHhhhhhhhccccccccccccccccccCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 456799999999999999988765443 2221211 22445679999999999888887
Q ss_pred Ccccccc
Q 023705 235 DEDALDE 241 (278)
Q Consensus 235 G~vmmn~ 241 (278)
....-|+
T Consensus 83 ~~~f~~m 89 (213)
T TIGR00865 83 RRAFSDM 89 (213)
T ss_pred HHHHHHH
Confidence 6655444
No 21
>PRK10072 putative transcriptional regulator; Provisional
Probab=63.57 E-value=6 Score=31.61 Aligned_cols=52 Identities=23% Similarity=0.249 Sum_probs=36.6
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc--Cccccccc-hhhhhhcccCC
Q 023705 201 LVVNLIQLRKASMLDDSQVAEILNEISRRFVREK--DEDALDEQ-PPMQALFVFDP 253 (278)
Q Consensus 201 ~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~--G~vmmn~~-~avqalf~~~~ 253 (278)
...|+-+||+..|+|..|+|+.|. ++.+-|.+| |.-.-+.. +..-.+.+++|
T Consensus 34 ~~~eik~LR~~~glTQ~elA~~lG-vS~~TVs~WE~G~r~P~~~~l~Ll~~L~~~P 88 (96)
T PRK10072 34 SFTEFEQLRKGTGLKIDDFARVLG-VSVAMVKEWESRRVKPSSAELKLMRLIQANP 88 (96)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHHHcCCCCCCHHHHHHHHHHhhCH
Confidence 456788888888999999998888 778877766 65544433 33445566666
No 22
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=63.21 E-value=30 Score=23.92 Aligned_cols=54 Identities=26% Similarity=0.395 Sum_probs=35.5
Q ss_pred HHHHHHHhCCChHHHHHHHHH-HHhc-----C---CCCChHHHHHHHHHHh--hcCCCcHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIR-YALN-----E---KPFNPDLVVNLIQLRK--ASMLDDSQVAEIL 223 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYir-Y~Ln-----E---r~F~pd~VaDLi~Lrk--as~L~D~evaEiL 223 (278)
++++.+++|.+.. .+|+|.. +-+. + +-|+++.|.-|..++. ..|++=+|+++.|
T Consensus 3 ~~eva~~~gvs~~-tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 3 IGAVARLTGVSPD-TLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHHCcCHH-HHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3567777777654 4567765 3331 2 5788887766544432 3899999999876
No 23
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=62.95 E-value=18 Score=31.55 Aligned_cols=37 Identities=24% Similarity=0.319 Sum_probs=27.0
Q ss_pred ChHHHHHHHHHHHhcCCCC-ChHHHHHHHHHHhhcCCC
Q 023705 179 SMEDVLRKYIRYALNEKPF-NPDLVVNLIQLRKASMLD 215 (278)
Q Consensus 179 s~~EV~RKYirY~LnEr~F-~pd~VaDLi~Lrkas~L~ 215 (278)
.+.|||+|-+.|+=+=--| |+++|.++.++=...||.
T Consensus 49 ~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~iLs~~~lh 86 (134)
T KOG2351|consen 49 EMSDVFKKTLQYLDRFSRFKNRETVRAVRTILSGKGLH 86 (134)
T ss_pred hHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHhhCCcc
Confidence 4788999998888664444 788888888776655543
No 24
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=62.73 E-value=28 Score=29.99 Aligned_cols=65 Identities=17% Similarity=0.151 Sum_probs=54.2
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHHHHhh
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQLRKA 211 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi~Lrka 211 (278)
...+.+-|.++|.+.+-.+++++++.|...+|.++..+ +.|-.=|+-++ +.|.+.|.+++.-...
T Consensus 113 ~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~-~It~e~I~~~~~~~~~ 180 (302)
T TIGR01128 113 EQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDG-KITLEDVEEAVSDSAR 180 (302)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCC-CCCHHHHHHHHhhhhc
Confidence 34566778999999998999999999999999998876 78888887666 7999999988865543
No 25
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=62.29 E-value=8.9 Score=28.97 Aligned_cols=78 Identities=21% Similarity=0.255 Sum_probs=53.1
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcC-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023705 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE-KPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (278)
Q Consensus 151 kSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnE-r~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srR 229 (278)
..|++||-++...--...+++|..+ .-..+|++.=|..+|.+ +.+++-...=|-+|-+.--++.+++.+.+.+.-+.
T Consensus 7 ~~l~ey~~~~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~ 84 (113)
T PF02847_consen 7 SILMEYFSSGDVDEAVECLKELKLP--SQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLES 84 (113)
T ss_dssp HHHHHHHHHT-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhH
Confidence 4678888886543333444554444 66789999999999999 44544444445578888889999999998876554
Q ss_pred h
Q 023705 230 F 230 (278)
Q Consensus 230 i 230 (278)
+
T Consensus 85 l 85 (113)
T PF02847_consen 85 L 85 (113)
T ss_dssp H
T ss_pred h
Confidence 4
No 26
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=61.77 E-value=32 Score=30.90 Aligned_cols=62 Identities=21% Similarity=0.203 Sum_probs=53.1
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
...+.+-|.+.+.+.+-.+++.+++.|...+|-++..+ +.|-.-|+-..++-|.+.|.+++.
T Consensus 144 ~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 144 ERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 56678889999999999999999999999999988665 678888877667899998887754
No 27
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=61.34 E-value=1e+02 Score=26.69 Aligned_cols=73 Identities=12% Similarity=0.168 Sum_probs=50.6
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEI 222 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEi 222 (278)
...+.+-|..++.+.+-.++.+++..|...+|-++..+ ++++..| .++-|.+.|.+++ ......+|-++
T Consensus 163 ~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~---~~~it~~~v~~~~-----~~~~~~~i~~l 234 (319)
T PRK00440 163 KEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT---GKEVTEEAVYKIT-----GTARPEEIREM 234 (319)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc---CCCCCHHHHHHHh-----CCCCHHHHHHH
Confidence 34567777888888777899999999999999988765 4555544 4678888887665 22333455555
Q ss_pred HHHH
Q 023705 223 LNEI 226 (278)
Q Consensus 223 LnE~ 226 (278)
++.+
T Consensus 235 ~~~~ 238 (319)
T PRK00440 235 IELA 238 (319)
T ss_pred HHHH
Confidence 5444
No 28
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=60.46 E-value=33 Score=30.14 Aligned_cols=64 Identities=14% Similarity=0.112 Sum_probs=52.3
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHHHHHh
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLIQLRK 210 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDLi~Lrk 210 (278)
...+.+-|.++|.+.+-.+++++++.|...+|-++..+-. |..-|+-+.+ .|.+.|..++.-..
T Consensus 148 ~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~~ 214 (340)
T PRK05574 148 EAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDSA 214 (340)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhhh
Confidence 4457778999999999999999999999999999887654 7777765544 99999988876533
No 29
>PF11166 DUF2951: Protein of unknown function (DUF2951); InterPro: IPR021337 This family of proteins has no known function. It has a highly conserved sequence.
Probab=60.37 E-value=5.9 Score=32.90 Aligned_cols=21 Identities=38% Similarity=0.804 Sum_probs=18.2
Q ss_pred hHHhhhhHhhhhhhhhhhhhhh
Q 023705 108 WILAVPLAYVGVSFVIAFVKTV 129 (278)
Q Consensus 108 wLlAlPLAylG~TFviA~vRtv 129 (278)
|++++--..+| ||+||+.||+
T Consensus 75 wilGlvgTi~g-sliia~lr~~ 95 (98)
T PF11166_consen 75 WILGLVGTIFG-SLIIALLRTI 95 (98)
T ss_pred HHHHHHHHHHH-HHHHHHHHHH
Confidence 88888777777 9999999996
No 30
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=60.23 E-value=22 Score=31.56 Aligned_cols=73 Identities=21% Similarity=0.286 Sum_probs=46.4
Q ss_pred hCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhh----------cCCCcHHHHHHHHHHHHhhhh--h--cCcccccc
Q 023705 176 TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKA----------SMLDDSQVAEILNEISRRFVR--E--KDEDALDE 241 (278)
Q Consensus 176 TGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrka----------s~L~D~evaEiLnE~srRiv~--~--~G~vmmn~ 241 (278)
..|+.++|||+ -++||+||.+.|.+.++.- +.++=+|+-++++++|+-.=. . .||=+=++
T Consensus 71 ~~y~l~~i~r~------a~~~vp~d~L~~~L~~~G~~ae~~~~~i~T~a~~eev~~l~~~Lse~~~e~~~~~~~~~aK~v 144 (190)
T PF09840_consen 71 YRYSLDDIFRE------AGYPVPPDLLVDALKLLGYKAEYREDVIKTDAPLEEVVELAERLSEIYKELRFQPLGTKAKRV 144 (190)
T ss_pred eEEcHHHHHHH------cCCCCCHHHHHHHHHhCCCeeEEeCCeEEecCCHHHHHHHHHHHHHHHHHHhcCccCHHHHHH
Confidence 45788999885 4599999999999998642 234445555555555543211 1 14433334
Q ss_pred chhhhhhcccCCc
Q 023705 242 QPPMQALFVFDPV 254 (278)
Q Consensus 242 ~~avqalf~~~~~ 254 (278)
-.++-+++|.||-
T Consensus 145 i~~~s~~~g~~p~ 157 (190)
T PF09840_consen 145 IAAVSYATGLDPE 157 (190)
T ss_pred HHHHHHHhCCCHH
Confidence 4677778888874
No 31
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=59.34 E-value=69 Score=25.10 Aligned_cols=55 Identities=16% Similarity=0.203 Sum_probs=32.9
Q ss_pred HHHHHHhCCChHHHHHHHHHH-Hh--------cCCCCChHHHHHHHHHHh---hcCCCcHHHHHHHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIRY-AL--------NEKPFNPDLVVNLIQLRK---ASMLDDSQVAEILNE 225 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYirY-~L--------nEr~F~pd~VaDLi~Lrk---as~L~D~evaEiLnE 225 (278)
.++.+.+|-|.. -+|.|-+- .+ |=|-|+++.|..|..++. ..|++=++|+++|++
T Consensus 4 ~EvA~~~gVs~~-tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 4 GEVAEILGLPPH-VLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred HHHHHHHCcCHH-HHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 345555665543 34444321 22 224588888887776663 578888888887774
No 32
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=59.11 E-value=31 Score=24.23 Aligned_cols=53 Identities=25% Similarity=0.353 Sum_probs=34.4
Q ss_pred HHHHHHhCCChHHHHHHHHH-HHh-------cCCCCChHHHHHHHH---HHhhcCCCcHHHHHHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIR-YAL-------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILN 224 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYir-Y~L-------nEr~F~pd~VaDLi~---Lrkas~L~D~evaEiLn 224 (278)
.++.+.+|-+.. -+|.|-+ +.+ +-|-|+++.|+.|.. ||. .|++=+||+++||
T Consensus 4 ~evA~~~gvs~~-tlR~~~~~g~l~~~~~~~g~R~y~~~~l~~l~~i~~l~~-~g~~l~~i~~~l~ 67 (67)
T cd04764 4 KEVSEIIGVKPH-TLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEILN 67 (67)
T ss_pred HHHHHHHCcCHH-HHHHHHHhcCCCCCCCCCCceeeCHHHHHHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 355556666554 3455543 222 335698888877655 455 8999999999885
No 33
>PHA01748 hypothetical protein
Probab=59.07 E-value=12 Score=27.53 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhcCCC
Q 023705 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKP 196 (278)
Q Consensus 168 vLk~L~~KTGFs~~EV~RKYirY~LnEr~ 196 (278)
.|..+..+.|++..|++|+.|+..+.|+.
T Consensus 16 eld~~a~~~g~~RSE~Ir~Ai~~~~~~~~ 44 (60)
T PHA01748 16 LLDRYAIKHGLNRSEAIRKAIEKMVKDEL 44 (60)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34567788999999999999998886643
No 34
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=58.91 E-value=27 Score=28.73 Aligned_cols=46 Identities=22% Similarity=0.465 Sum_probs=28.5
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH------HhhhhhcCcccccc
Q 023705 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS------RRFVREKDEDALDE 241 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s------rRiv~~~G~vmmn~ 241 (278)
+++|+.+++|+.|=..=.+|.+.+.++|.+.. ..|+++||+..++-
T Consensus 38 ~i~~~~l~~li~lv~~g~It~~~ak~vl~~~~~~~~~~~~ii~~~~l~~isd 89 (147)
T smart00845 38 PITPEHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEEIVEEKGLKQISD 89 (147)
T ss_pred CCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCHHHHHHHcCCccCCC
Confidence 56666666666666666666666666666553 35666666665543
No 35
>COG4174 ABC-type uncharacterized transport system, permease component [General function prediction only]
Probab=58.82 E-value=13 Score=36.39 Aligned_cols=50 Identities=24% Similarity=0.484 Sum_probs=44.5
Q ss_pred CCCCCCchHHHHHHHHhCCCh------HHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 023705 160 GGDAVNPPALKGLVQKTGFSM------EDVLRKYIRYALNEKPFNPDLVVNLIQLR 209 (278)
Q Consensus 160 gRdal~~gvLk~L~~KTGFs~------~EV~RKYirY~LnEr~F~pd~VaDLi~Lr 209 (278)
|+.++++..+++|++..||+- -..+-+|+|+-.-|.-|-..-|-|||.=|
T Consensus 76 g~~GlDpe~i~~i~~~~GFDKp~~eR~~~Ml~~y~rfDfGeS~fr~~~VidLI~ek 131 (364)
T COG4174 76 GAQGLDPELIAEIEKQYGFDKPPLERYFLMLWDYARFDFGESFFRDASVIDLIKEK 131 (364)
T ss_pred cccCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhccccHHhhcCChHHHHHHHh
Confidence 667899999999999999995 35678999999999999999999999755
No 36
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=57.62 E-value=41 Score=29.97 Aligned_cols=59 Identities=24% Similarity=0.320 Sum_probs=51.4
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHh-cCCCCChHHHHHHHH
Q 023705 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYAL-NEKPFNPDLVVNLIQ 207 (278)
Q Consensus 149 LvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~L-nEr~F~pd~VaDLi~ 207 (278)
+.+-|.+.+.+.+-.++..+++.|...+|.++..+ +.|-+-|+. ..++-|++.|..++.
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~ 197 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVS 197 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhc
Confidence 67788999999898899999999999999999988 678877764 466799999999875
No 37
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=57.33 E-value=18 Score=27.04 Aligned_cols=33 Identities=21% Similarity=0.414 Sum_probs=27.6
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q 023705 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFV 231 (278)
Q Consensus 198 ~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv 231 (278)
|.-.|..||.|.. ...+|.++.++|.++..||.
T Consensus 9 nLq~i~sll~lq~-~~~~~~e~~~~L~~~~~RI~ 41 (76)
T PF07568_consen 9 NLQIISSLLRLQA-RRSEDPEAREALEDAQNRIQ 41 (76)
T ss_pred HHHHHHHHHHHHH-hcCCCHHHHHHHHHHHHHHH
Confidence 4567889999984 56799999999999999974
No 38
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=57.29 E-value=13 Score=29.40 Aligned_cols=24 Identities=17% Similarity=0.106 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 201 LVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 201 ~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
+...+.+.|+.+|||-.|||+.++
T Consensus 12 ~~~~lk~~R~~lGLTQ~dvA~~lg 35 (75)
T smart00352 12 FAKTFKQRRIKLGFTQADVGLALG 35 (75)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhc
Confidence 456788999999999999999887
No 39
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=56.85 E-value=64 Score=28.17 Aligned_cols=76 Identities=9% Similarity=0.140 Sum_probs=53.3
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCC-cHHHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLD-DSQVAEILNE 225 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~-D~evaEiLnE 225 (278)
..+.+-|.+.+.+.+-.++..+++.|...+|-++.+++.---.|+...+..|.+.|.+++.- .+ ++.|-++++.
T Consensus 187 ~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~~~~~~-----~~~~~~i~~l~~a 261 (337)
T PRK12402 187 DELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEALGD-----VGTDEVIESLLDA 261 (337)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCC-----CCCHHHHHHHHHH
Confidence 35677788888887777999999999999999999987644445555567787777664321 12 4456555554
Q ss_pred HH
Q 023705 226 IS 227 (278)
Q Consensus 226 ~s 227 (278)
++
T Consensus 262 i~ 263 (337)
T PRK12402 262 AE 263 (337)
T ss_pred HH
Confidence 43
No 40
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=56.40 E-value=39 Score=25.65 Aligned_cols=84 Identities=20% Similarity=0.256 Sum_probs=59.0
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCC-CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023705 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEK-PFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (278)
Q Consensus 151 kSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr-~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srR 229 (278)
..|++||..+...--...|++|..+ .-.-|+++.-|-.+|.|+ .+++-...=|-+|.+...++.+++.+.+.++
T Consensus 7 ~~l~ey~~~~D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~--- 81 (113)
T smart00544 7 LIIEEYLSSGDTDEAVHCLLELKLP--EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWRL--- 81 (113)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHH---
Confidence 4688898776443333444454444 357899999999999996 5766666666678888889999999888764
Q ss_pred hhhhcCccccc
Q 023705 230 FVREKDEDALD 240 (278)
Q Consensus 230 iv~~~G~vmmn 240 (278)
++.-..+.+|
T Consensus 82 -~~~l~dl~~D 91 (113)
T smart00544 82 -LEDIEDLELD 91 (113)
T ss_pred -HhhChhhhcc
Confidence 4444445554
No 41
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=56.23 E-value=13 Score=35.16 Aligned_cols=48 Identities=25% Similarity=0.279 Sum_probs=39.1
Q ss_pred CCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 023705 160 GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (278)
Q Consensus 160 gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE 225 (278)
-|.+++.--|++|++.+- .-||| .|+|=++|=..+||||.||+---.-
T Consensus 175 sRTaFT~~Ql~~LEkrF~------~QKYL------------S~~DR~~LA~~LgLTdaQVKtWfQN 222 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFE------KQKYL------------SVADRIELAASLGLTDAQVKTWFQN 222 (309)
T ss_pred chhhhhHHHHHHHHHHHH------Hhhcc------------cHHHHHHHHHHcCCchhhHHHHHhh
Confidence 467788888889988764 46887 5889999999999999999866543
No 42
>KOG2499 consensus Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism]
Probab=55.10 E-value=14 Score=38.16 Aligned_cols=51 Identities=35% Similarity=0.677 Sum_probs=42.3
Q ss_pred hhcchhhHHhhH---------HHHHhcCCCCCCc------hHHHHHHHHhCCChHH--HHHHHHHHHh
Q 023705 142 LVNKNAMVCKTI---------DELFQKGGDAVNP------PALKGLVQKTGFSMED--VLRKYIRYAL 192 (278)
Q Consensus 142 ~VNKNamLvkSL---------DeyFp~gRdal~~------gvLk~L~~KTGFs~~E--V~RKYirY~L 192 (278)
+.|++=.+++.| |+||+-|+|+++. +..|+.|+|-||..++ ..|+|+.+++
T Consensus 306 ~~n~tydvls~i~~dv~evFp~~~~HlGGDEV~~~CW~s~~~Iq~fM~~kGfg~~~~~~~~~~~~~~~ 373 (542)
T KOG2499|consen 306 TNNHTYDVLSEIFEDVSEVFPDEFFHLGGDEVSTPCWKSNPEIQDFMRKKGFGLDTKSLERLYIQFLL 373 (542)
T ss_pred CchhHHHHHHHHHHHHHHhCcHHHeecCCceeecccccCChHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence 456666666665 7899999999965 5899999999999998 8999998875
No 43
>PF02417 Chromate_transp: Chromate transporter; InterPro: IPR003370 This entry represents chromate transporters (CHR) [, ]. These proteins reduce chromate accumulation and are essential for chromate resistance. They are composed of one or two copies of this region. The short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm, while the long chain CHR proteins appear to have arisen from a gene fusion event of two short chain transporters[].; GO: 0015109 chromate transmembrane transporter activity, 0015703 chromate transport
Probab=54.36 E-value=8.8 Score=32.07 Aligned_cols=65 Identities=20% Similarity=0.357 Sum_probs=38.8
Q ss_pred HHHHhcchhhHHhhhhhhhhccccccccCCCc-------CCCCCchhHHhhhhHhh----hhhhhhhhhhhhhhcCChh
Q 023705 69 VEVEEELPWIQEKALDLVEFTGSVTQAIPGPR-------VGQSKLPWILAVPLAYV----GVSFVIAFVKTVKKFNSPK 136 (278)
Q Consensus 69 ~e~e~e~~wiqekaldlveftG~vtQAIPGPR-------Vg~s~lPwLlAlPLAyl----G~TFviA~vRtvrK~~SPr 136 (278)
+|.-++..||.|+-. .|.. .+.|.+|||- +|-.--.|++|+-.... +..+++.+...++++.+.+
T Consensus 29 ~~~V~~~~wlt~~~f--~~~~-al~q~~PGP~~~n~a~~iG~~~~G~~Gai~a~~~~~lP~~l~~~~~~~~~~~~~~~~ 104 (169)
T PF02417_consen 29 REFVERRGWLTEEEF--LEGL-ALAQALPGPIAINLATFIGYRLAGFLGAIVATIGFILPSFLLILLLSPLYSRFRENP 104 (169)
T ss_pred HHHhHccCCCCHHHH--HHHH-HHHHcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccH
Confidence 344456788876532 2222 4689999994 34444556666543322 4556677778888887533
No 44
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=54.01 E-value=41 Score=26.91 Aligned_cols=69 Identities=22% Similarity=0.205 Sum_probs=45.7
Q ss_pred hcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCcc
Q 023705 158 QKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDED 237 (278)
Q Consensus 158 p~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~v 237 (278)
++-....-..+++.|..+.|.|.++|.+ -++ ++|-.+-...| ...-|+.|.++++.+.++|+..
T Consensus 11 q~~s~~~a~~~~~~l~~~~gpt~~~l~~-----------~~~---~~l~~~~~~~G--~~~kA~~i~~~a~~~~~~~~~~ 74 (158)
T cd00056 11 QQTTDKAVNKAYERLFERYGPTPEALAA-----------ADE---EELRELIRSLG--YRRKAKYLKELARAIVEGFGGL 74 (158)
T ss_pred hcccHHHHHHHHHHHHHHhCCCHHHHHC-----------CCH---HHHHHHHHhcC--hHHHHHHHHHHHHHHHHHcCCc
Confidence 3444444556677777777755544433 122 44555666666 5678999999999999999987
Q ss_pred ccccc
Q 023705 238 ALDEQ 242 (278)
Q Consensus 238 mmn~~ 242 (278)
..+.+
T Consensus 75 ~~~~~ 79 (158)
T cd00056 75 VLDDP 79 (158)
T ss_pred cCCCc
Confidence 74444
No 45
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=53.57 E-value=14 Score=24.40 Aligned_cols=23 Identities=13% Similarity=0.427 Sum_probs=19.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCh
Q 023705 177 GFSMEDVLRKYIRYALNEKPFNP 199 (278)
Q Consensus 177 GFs~~EV~RKYirY~LnEr~F~p 199 (278)
+++..|++-+||.|.|..+-+..
T Consensus 2 ~~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 2 RLDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred CcchHHHHHHHHHHHHhhcCCCC
Confidence 68899999999999998876543
No 46
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=53.31 E-value=5.8 Score=32.30 Aligned_cols=10 Identities=30% Similarity=0.547 Sum_probs=5.4
Q ss_pred hHHHHhcchh
Q 023705 68 EVEVEEELPW 77 (278)
Q Consensus 68 e~e~e~e~~w 77 (278)
|||+|++|.|
T Consensus 93 ~eE~dddmgf 102 (105)
T cd04411 93 EEEEDEDFGF 102 (105)
T ss_pred ccccccccCc
Confidence 3444556765
No 47
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=53.26 E-value=1 Score=34.56 Aligned_cols=7 Identities=14% Similarity=0.511 Sum_probs=2.7
Q ss_pred HHHHhcc
Q 023705 69 VEVEEEL 75 (278)
Q Consensus 69 ~e~e~e~ 75 (278)
||+|++|
T Consensus 77 EEed~dm 83 (88)
T PF00428_consen 77 EEEDDDM 83 (88)
T ss_dssp SS-SSSS
T ss_pred ccccccc
Confidence 3444444
No 48
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=52.77 E-value=38 Score=29.80 Aligned_cols=59 Identities=27% Similarity=0.388 Sum_probs=45.2
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhh-cCCCcHHHHHHHHHHHHhhhhhcCccccccc
Q 023705 182 DVLRKYIRYALNEKPFNPDLVVNLIQLRKA-SMLDDSQVAEILNEISRRFVREKDEDALDEQ 242 (278)
Q Consensus 182 EV~RKYirY~LnEr~F~pd~VaDLi~Lrka-s~L~D~evaEiLnE~srRiv~~~G~vmmn~~ 242 (278)
+-.+|=||-.|.++.|+++.|++.|+-=.. --|||.+.||.. +..|+-+-|||..+--+
T Consensus 34 ~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~--i~~r~~~g~G~~rl~qe 93 (174)
T COG2137 34 DRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAY--IRSRSRKGKGPARLKQE 93 (174)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHH--HHHHHhcccChHHHHHH
Confidence 556677788899999999999999985444 457999999975 44555555898876544
No 49
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=52.76 E-value=41 Score=24.56 Aligned_cols=39 Identities=15% Similarity=0.304 Sum_probs=27.6
Q ss_pred chHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023705 166 PPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 166 ~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi 206 (278)
...+.+|... ||+..+|++.-.++.++- .+++.....++
T Consensus 24 ~~~~~~l~~~-G~s~~~Il~~l~~~l~~~-~~~~~~k~~i~ 62 (89)
T PF08542_consen 24 RKKLYELLVE-GYSASDILKQLHEVLVES-DIPDSQKAEIL 62 (89)
T ss_dssp HHHHHHHHHT-T--HHHHHHHHHHHHHTS-TSSHHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHHHHh-hccHHHHHHHH
Confidence 3456777777 999999999999988887 66665555443
No 50
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=51.78 E-value=64 Score=24.21 Aligned_cols=55 Identities=22% Similarity=0.326 Sum_probs=36.5
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh--------cCCCCChHHHHHHH---HHHhhcCCCcHHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYAL--------NEKPFNPDLVVNLI---QLRKASMLDDSQVAEILNE 225 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~L--------nEr~F~pd~VaDLi---~Lrkas~L~D~evaEiLnE 225 (278)
++++..++|-+.. -+|.|.+.-+ +.+-|+++.|..+- .||+ .|++-++|+.+|..
T Consensus 3 ~~eva~~~gi~~~-tlr~~~~~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~-~g~~~~~i~~~l~~ 68 (100)
T cd00592 3 IGEVAKLLGVSVR-TLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLDA 68 (100)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCcCCCcCCCCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHHHHhc
Confidence 3566677777654 4466666544 44568887776654 4555 89999998888853
No 51
>PF11836 DUF3356: Protein of unknown function (DUF3356); InterPro: IPR021791 This entry consists of bacterial and phage proteins whose function is not currently known. Many of the bacterial sequences are found within known or suspected prophages or gene transfer agents (GTA). Gene transfer agents are related to bacteriophages, but are distinguished by cellular regulatory mechanisms that strongly suggest they are more than just defective prophages [, ].
Probab=50.82 E-value=42 Score=26.90 Aligned_cols=67 Identities=15% Similarity=0.115 Sum_probs=47.0
Q ss_pred CCCchHHHHHHHHhCC-ChHHHHHHHHHHHhcCCCCChHHHHHHHH--HHhh-cCCCcHHHHHHHHHHHHhhhhhcCccc
Q 023705 163 AVNPPALKGLVQKTGF-SMEDVLRKYIRYALNEKPFNPDLVVNLIQ--LRKA-SMLDDSQVAEILNEISRRFVREKDEDA 238 (278)
Q Consensus 163 al~~gvLk~L~~KTGF-s~~EV~RKYirY~LnEr~F~pd~VaDLi~--Lrka-s~L~D~evaEiLnE~srRiv~~~G~vm 238 (278)
.++.++|.+|+.++|= +..+++.+ +++..|.-+.|..+|. ||.+ .-.+++++.+ +|-+-||+-
T Consensus 17 ~LtlgaLaeLE~~~g~~~l~aL~~R-----f~~g~~s~~Dv~~vi~~GL~GgG~~~~~a~l~~--------~~~~~gp~~ 83 (101)
T PF11836_consen 17 RLTLGALAELEAALGAGGLFALVER-----FETGRFSARDVRAVIRAGLIGGGMPPTEADLVR--------AYVEGGPAA 83 (101)
T ss_pred eCCHHHHHHHHHHcCCCCHHHHHHH-----HhcCCCCHHHHHHHHHHHhcCCCCCCCHHHHHH--------hhhcCccHH
Confidence 3788999999999999 99999887 6788899988888886 3443 2334433332 344556665
Q ss_pred cccc
Q 023705 239 LDEQ 242 (278)
Q Consensus 239 mn~~ 242 (278)
-+..
T Consensus 84 ~~~~ 87 (101)
T PF11836_consen 84 AVAP 87 (101)
T ss_pred hHHH
Confidence 5444
No 52
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=49.00 E-value=47 Score=24.02 Aligned_cols=27 Identities=4% Similarity=0.051 Sum_probs=11.5
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023705 196 PFNPDLVVNLIQLRKASMLDDSQVAEI 222 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L~D~evaEi 222 (278)
..+|..++.++-.=+.-|.|.+|++..
T Consensus 31 ~~s~~qiaAfL~al~~kget~~Eiag~ 57 (66)
T PF02885_consen 31 EVSDAQIAAFLMALRMKGETPEEIAGF 57 (66)
T ss_dssp SS-HHHHHHHHHHHHHH---HHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhCcCHHHHHHH
Confidence 344555555444444455555555543
No 53
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=48.48 E-value=14 Score=24.60 Aligned_cols=27 Identities=37% Similarity=0.460 Sum_probs=19.6
Q ss_pred HHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023705 206 IQLRKASMLDDSQVAEILNEISRRFVRE 233 (278)
Q Consensus 206 i~Lrkas~L~D~evaEiLnE~srRiv~~ 233 (278)
-++|+..|+|-.|+|+.++ +++..+.+
T Consensus 2 k~~r~~~gls~~~la~~~g-is~~~i~~ 28 (55)
T PF01381_consen 2 KELRKEKGLSQKELAEKLG-ISRSTISR 28 (55)
T ss_dssp HHHHHHTTS-HHHHHHHHT-S-HHHHHH
T ss_pred HHHHHHcCCCHHHHHHHhC-CCcchhHH
Confidence 3678899999999999987 66665554
No 54
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=48.36 E-value=65 Score=29.72 Aligned_cols=63 Identities=19% Similarity=0.008 Sum_probs=38.4
Q ss_pred chHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH----HHhhcCCCcHHHHHHHHHHHHh
Q 023705 166 PPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ----LRKASMLDDSQVAEILNEISRR 229 (278)
Q Consensus 166 ~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~----Lrkas~L~D~evaEiLnE~srR 229 (278)
.+-|+-..+|+|.+.+|..++.-|.+.++-.=--|+..+.+. .=..++++ +++++.|.++++|
T Consensus 101 ~~il~~~a~~~~~~~e~~~~~~~~~l~~~yg~~y~af~~~~~~~~~~l~~~~~~-~~~~~~l~~~~~~ 167 (262)
T PRK03987 101 DKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEEALDDLGVP-EEWADALVEIARE 167 (262)
T ss_pred hhHHHHHHHHcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHhcChhhhccCCCC-HHHHHHHHHHHHH
Confidence 367889999999999999999999877762211112222111 12233455 5556666665555
No 55
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=47.73 E-value=56 Score=22.78 Aligned_cols=53 Identities=19% Similarity=0.197 Sum_probs=34.0
Q ss_pred HHHHHHHHhCCChHHHHH------HHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHH
Q 023705 168 ALKGLVQKTGFSMEDVLR------KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAE 221 (278)
Q Consensus 168 vLk~L~~KTGFs~~EV~R------KYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaE 221 (278)
.|+.+..+.|+|..|+-+ .||+..-+-+...| ....+..|=.++|++++++++
T Consensus 5 ~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p-~~~~l~~l~~~l~~~~~~~~~ 63 (64)
T PF13560_consen 5 RLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRP-SPDTLQRLARALGVPPDERAE 63 (64)
T ss_dssp HHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS--BHHHHHHHHHHTT--HHHHHC
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCC-CHHHHHHHHHHHCcCHHHHcc
Confidence 466677777777777654 47888888777644 234566667789999888764
No 56
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=47.29 E-value=1e+02 Score=31.00 Aligned_cols=61 Identities=13% Similarity=0.187 Sum_probs=48.6
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhc-CCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALN-EKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~Ln-Er~F~pd~VaDLi 206 (278)
...+.+.|...+.+.+-.++..++..|.+.++-|+-++ +.|.+-|.-. .+.-|.+.|.+++
T Consensus 189 ~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~ll 253 (507)
T PRK06645 189 FEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQML 253 (507)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHH
Confidence 45677888888888888899999999999999999877 6677777653 3457777777765
No 57
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=47.02 E-value=39 Score=28.97 Aligned_cols=79 Identities=11% Similarity=0.126 Sum_probs=49.5
Q ss_pred cCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhc-CCCCChHHHHHHHHHHh
Q 023705 132 FNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN-EKPFNPDLVVNLIQLRK 210 (278)
Q Consensus 132 ~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~Ln-Er~F~pd~VaDLi~Lrk 210 (278)
.+.++.+|++..+....|++.+++.+..-|.+..-. .++|.++.|.+ +.||.-.-| +...+.+ .+.+|=+
T Consensus 49 ~~~~~~~~~~~~d~~~~l~~~~g~~Ir~~Re~~glS-qeeLA~~lgvs-----~s~IsriE~G~~~Ps~~---~l~kLa~ 119 (154)
T TIGR00270 49 ARKPVKRKRRKIDTTEELVEDYGIIIRREREKRGWS-QEQLAKKIQEK-----ESLIKKIENAEIEPEPK---VVEKLEK 119 (154)
T ss_pred CCCCCCCCCCccchHHHHHHHHHHHHHHHHHHcCCC-HHHHHHHhCCC-----HHHHHHHHCCCCCCCHH---HHHHHHH
Confidence 344455555566667778888888877766654443 56777777776 455655554 3444444 4556667
Q ss_pred hcCCCcHHH
Q 023705 211 ASMLDDSQV 219 (278)
Q Consensus 211 as~L~D~ev 219 (278)
++|.+-.+.
T Consensus 120 ~Lgvsl~el 128 (154)
T TIGR00270 120 LLKIKLREQ 128 (154)
T ss_pred HhCCCHHHH
Confidence 888776653
No 58
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=46.50 E-value=50 Score=26.90 Aligned_cols=65 Identities=23% Similarity=0.316 Sum_probs=40.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHhhhhhcCccccc
Q 023705 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASM-LDDSQVAEILNEISRRFVREKDEDALD 240 (278)
Q Consensus 168 vLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~-L~D~evaEiLnE~srRiv~~~G~vmmn 240 (278)
+|+-|..+ .+|..|| +-.|.++-|+++.+++.|+-=+..| |+|...|+..-..-.+ +.+|+-.+-
T Consensus 17 al~~L~~r-~~s~~el-----~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~--~~~g~~~I~ 82 (157)
T PRK00117 17 ALRLLARR-EHSRAEL-----RRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRAR--KGYGPRRIR 82 (157)
T ss_pred HHHHHccc-hhHHHHH-----HHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh--CCchHHHHH
Confidence 34444433 5565555 4446777888888888887555555 7777888776544322 567765543
No 59
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=46.00 E-value=21 Score=29.81 Aligned_cols=49 Identities=24% Similarity=0.373 Sum_probs=37.1
Q ss_pred cccCCCcCCCCCchhHHhhhhHhhhhhhhhhhh---hhhhh-cCChhhhhhhh
Q 023705 94 QAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFV---KTVKK-FNSPKFKRKKL 142 (278)
Q Consensus 94 QAIPGPRVg~s~lPwLlAlPLAylG~TFviA~v---RtvrK-~~SPraKRkR~ 142 (278)
...|+|.-|+-+.|.|.++-++-+.++++|++. .+++| +.|=|++|-..
T Consensus 5 ~~~~~~~~~g~sW~~LVGVv~~al~~SlLIalaaKC~~~~k~~~SY~H~rL~e 57 (102)
T PF15176_consen 5 ANAPGPGEGGRSWPFLVGVVVTALVTSLLIALAAKCPVWYKYLASYRHHRLPE 57 (102)
T ss_pred ccCCCCCCCCcccHhHHHHHHHHHHHHHHHHHHHHhHHHHHHHhccccccCCc
Confidence 456999999999999999999999999999874 23333 45556655443
No 60
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=45.89 E-value=86 Score=34.55 Aligned_cols=78 Identities=22% Similarity=0.356 Sum_probs=54.1
Q ss_pred hhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHH---hCCChHHHHHHHHHHHhcCCCCChHHHHHHHH-HHhhcCCC-
Q 023705 141 KLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQK---TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ-LRKASMLD- 215 (278)
Q Consensus 141 R~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~K---TGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~-Lrkas~L~- 215 (278)
+.|..|..=..-|..+..++|+ ++...|++|+.+ -||+-+.+-+-|= +.. |.|..||||. .|.|.|++
T Consensus 966 ~~i~~~~~~i~al~~~~~~p~~-lt~~~l~~l~~~l~~~~~~~~~l~~a~~-----~~~-~~~~~a~ii~~iR~~~~~~~ 1038 (1123)
T PRK11448 966 AFVRENINQIPALQVVVNRPRD-LTRKELKELRLLLDQQGFSEASLRSAWK-----ETK-NEDIAASIIGFIRQAALGDA 1038 (1123)
T ss_pred HHHHhcccccHHHHHHHhCCcc-CCHHHHHHHHHHhhhCCCCHHHHHHHHH-----hch-hhhHHHHHHHHHHHHhcCCc
Confidence 3444455555556666666644 999999998843 4888776665543 222 8899999997 49999998
Q ss_pred ----cHHHHHHHHH
Q 023705 216 ----DSQVAEILNE 225 (278)
Q Consensus 216 ----D~evaEiLnE 225 (278)
++-|.++++.
T Consensus 1039 l~~~~~~v~~a~~~ 1052 (1123)
T PRK11448 1039 LVPFEERVDHAMQK 1052 (1123)
T ss_pred CCCHHHHHHHHHHH
Confidence 6777777666
No 61
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=45.84 E-value=17 Score=28.02 Aligned_cols=40 Identities=20% Similarity=0.441 Sum_probs=33.8
Q ss_pred HHHhhcCC-CcHHHHHHHHHHHHhhhhhcCccccccchhhhhhcccCCccch
Q 023705 207 QLRKASML-DDSQVAEILNEISRRFVREKDEDALDEQPPMQALFVFDPVHNI 257 (278)
Q Consensus 207 ~Lrkas~L-~D~evaEiLnE~srRiv~~~G~vmmn~~~avqalf~~~~~~~~ 257 (278)
.+|...|- ||+||-..|.|-. ||-..|+|-|.+.||+|..
T Consensus 11 ~iKEiv~~hse~eIya~L~ecn-----------MDpnea~qrLL~qD~FheV 51 (60)
T PF06972_consen 11 SIKEIVGCHSEEEIYAMLKECN-----------MDPNEAVQRLLSQDPFHEV 51 (60)
T ss_pred HHHHHhcCCCHHHHHHHHHHhC-----------CCHHHHHHHHHhcCcHHHH
Confidence 36778888 9999999998853 7777999999999999864
No 62
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=45.44 E-value=86 Score=25.77 Aligned_cols=80 Identities=13% Similarity=0.160 Sum_probs=49.3
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHHH----HHHHhcCCCCChHHHHHHHHH--------------HhhcCCCcHHHHHH
Q 023705 161 GDAVNPPALKGLVQKTGFSMEDVLRKY----IRYALNEKPFNPDLVVNLIQL--------------RKASMLDDSQVAEI 222 (278)
Q Consensus 161 Rdal~~gvLk~L~~KTGFs~~EV~RKY----irY~LnEr~F~pd~VaDLi~L--------------rkas~L~D~evaEi 222 (278)
.+.++...|+.+..++|.+.++++++= -.-.+.+...+.+.+-++|.= +-..|.+++++.++
T Consensus 34 ~~~~s~~eL~~~l~~~~~~~~~lin~~~~~~k~L~~~~~~ls~~e~i~ll~~~P~LikRPIv~~~~~~~iG~~~e~~~~~ 113 (132)
T PRK13344 34 KEPLTKEEILAILTKTENGIESIVSSKNRYAKALDCDIEELSVNEVIDLIQENPRILKSPILIDDKRLQVGYKEDDIRAF 113 (132)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHhhccCcHHHHhCCcchhcCCHHHHHHHHHhCccceeCcEEEeCCEEEeCCCHHHHHHH
Confidence 467899999999999999999999862 222222334444444444431 23467777777777
Q ss_pred HHHHHHhhhhhcCccccc
Q 023705 223 LNEISRRFVREKDEDALD 240 (278)
Q Consensus 223 LnE~srRiv~~~G~vmmn 240 (278)
|.-.-|+.--+..++|.|
T Consensus 114 l~~~~r~~~~~~~~~~~~ 131 (132)
T PRK13344 114 LPRSIRNVENAEARLRAA 131 (132)
T ss_pred ccHHHHHHHHHHhHHhhc
Confidence 754445554444444433
No 63
>PRK14038 ADP-dependent glucokinase; Provisional
Probab=44.54 E-value=22 Score=35.66 Aligned_cols=104 Identities=15% Similarity=0.250 Sum_probs=68.0
Q ss_pred hcCChhhhh----hhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhc--CC--------C
Q 023705 131 KFNSPKFKR----KKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN--EK--------P 196 (278)
Q Consensus 131 K~~SPraKR----kR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~Ln--Er--------~ 196 (278)
.|++||+-| .+..|-..++.+.+.++|+.-....+--+|-|++.=.+++..|.|++=.+.... ++ +
T Consensus 188 ~~~aPRaNRfI~s~D~~N~~l~~~eef~~~l~ei~~~~Dl~vlSG~q~l~~~~~~~~l~~~~~~l~~l~~~~i~iH~EfA 267 (453)
T PRK14038 188 DFEAPRENRFIGAADDYNPNLYIRPEFRERFEEIAKKAELAIISGLQALTEENYREPFETVREHLKVLNERGIPAHLEFA 267 (453)
T ss_pred eeEcCCCceEEEecCCCCcceeecHHHHHHHHhhccCCCEEEEEchhhhccccHHHHHHHHHHHHHhcCcCCceEEEEee
Confidence 799999988 566777777888888888875455666666666655567666666665554433 32 2
Q ss_pred CC--hHHHHHHHHHHh---hcCCCcHHHHHHHH-----HHHHhhhhhc
Q 023705 197 FN--PDLVVNLIQLRK---ASMLDDSQVAEILN-----EISRRFVREK 234 (278)
Q Consensus 197 F~--pd~VaDLi~Lrk---as~L~D~evaEiLn-----E~srRiv~~~ 234 (278)
|. .+...+++.+=. -.||+..|++-+++ |.|+||.+.+
T Consensus 268 s~~d~~~r~~i~~ilp~vDSlGmNE~ELa~ll~~lg~~~l~~~i~~~~ 315 (453)
T PRK14038 268 FTPDETVREEILGLLGKFYSVGLNEVELASIMEVMGEKTLAEKLLAKD 315 (453)
T ss_pred ccchHHHHHHHHhhCccccccccCHHHHHHHHHHhccchhhhhhhhcC
Confidence 22 222333332221 27899999999997 6788888743
No 64
>PF12446 DUF3682: Protein of unknown function (DUF3682); InterPro: IPR022152 This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length.
Probab=44.53 E-value=11 Score=32.67 Aligned_cols=16 Identities=38% Similarity=0.370 Sum_probs=8.6
Q ss_pred hchhhhhhHHHHhcch
Q 023705 61 KKKAEEVEVEVEEELP 76 (278)
Q Consensus 61 ~~~~~e~e~e~e~e~~ 76 (278)
-+++||+|||+|.|+.
T Consensus 93 h~rqEeeEEeEe~Ekq 108 (133)
T PF12446_consen 93 HTRQEEEEEEEENEKQ 108 (133)
T ss_pred ccchhhhhhhhhhhhh
Confidence 3455555566666653
No 65
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=44.21 E-value=23 Score=26.93 Aligned_cols=28 Identities=39% Similarity=0.554 Sum_probs=22.2
Q ss_pred CChHHHHHHHH-HHhhcCCCcHHHHHHHHH
Q 023705 197 FNPDLVVNLIQ-LRKASMLDDSQVAEILNE 225 (278)
Q Consensus 197 F~pd~VaDLi~-Lrkas~L~D~evaEiLnE 225 (278)
.++|.|.|+|- |.| -|++.+||.-||+|
T Consensus 28 ~~~~eVe~~I~klak-kG~tpSqIG~iLRD 56 (60)
T PF08069_consen 28 YSPEEVEELIVKLAK-KGLTPSQIGVILRD 56 (60)
T ss_dssp S-HHHHHHHHHHHCC-TTHCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-cCCCHHHhhhhhhh
Confidence 57788888764 544 89999999999997
No 66
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.21 E-value=35 Score=29.66 Aligned_cols=44 Identities=16% Similarity=0.145 Sum_probs=30.9
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 178 FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 178 Fs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
...+.++++||+..... +...+.=|-+|..-.-+||+|+|+.|.
T Consensus 4 ~~~~~~v~~~l~~~~~~---~~~~~~Vl~~L~~~g~~tdeeLA~~Lg 47 (178)
T PRK06266 4 MLNNPLVQKVLFEIMEG---DEEGFEVLKALIKKGEVTDEEIAEQTG 47 (178)
T ss_pred hhcCHHHHHHHHHHhcC---CccHhHHHHHHHHcCCcCHHHHHHHHC
Confidence 44567899999998874 323343344566656799999999873
No 67
>KOG1577 consensus Aldo/keto reductase family proteins [General function prediction only]
Probab=43.06 E-value=70 Score=30.69 Aligned_cols=64 Identities=22% Similarity=0.358 Sum_probs=53.5
Q ss_pred CCCCchHHHHHHHHhCCChHHHHHHHHHHHhcC------CCCChHHHHHHHHHHhhcCCCcHHHHHHH-HHHHHh
Q 023705 162 DAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE------KPFNPDLVVNLIQLRKASMLDDSQVAEIL-NEISRR 229 (278)
Q Consensus 162 dal~~gvLk~L~~KTGFs~~EV~RKYirY~LnE------r~F~pd~VaDLi~Lrkas~L~D~evaEiL-nE~srR 229 (278)
+-+..+.++.|.+|.|=|-..|+ |||++.- |-+||+-+.+=++.-. ..||++|++.|- .....|
T Consensus 218 ~ll~~~~l~~iA~K~~kt~aQIl---Lrw~~q~g~~vipKS~~~~Ri~eN~~vfd-f~Lt~ed~~~i~~~~~~~r 288 (300)
T KOG1577|consen 218 DLLEDPVLKEIAKKYNKTPAQIL---LRWALQRGVSVIPKSSNPERIKENFKVFD-FELTEEDMKKLDSLNSNER 288 (300)
T ss_pred ccccCHHHHHHHHHhCCCHHHHH---HHHHHhCCcEEEeccCCHHHHHHHHhhcc-ccCCHHHHHHHhhccccce
Confidence 45889999999999999999998 7888876 6899999988888655 889999999987 334444
No 68
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=42.94 E-value=51 Score=21.82 Aligned_cols=38 Identities=13% Similarity=0.179 Sum_probs=23.9
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023705 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (278)
Q Consensus 145 KNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV 183 (278)
....-..-|.++|..+. -.+...+..|...+|-+...|
T Consensus 7 ~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~l~~~qV 44 (59)
T cd00086 7 FTPEQLEELEKEFEKNP-YPSREEREELAKELGLTERQV 44 (59)
T ss_pred CCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHCcCHHHH
Confidence 33444556667777755 466667777777777666555
No 69
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=42.90 E-value=1.7e+02 Score=27.60 Aligned_cols=61 Identities=21% Similarity=0.279 Sum_probs=46.8
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHh---cCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYAL---NEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~L---nEr~F~pd~VaDLi 206 (278)
...+.+.|.+.+.+.+-.++..++..|...+|-++..+.+ |=+.|+. ..+.-+.+.|.+++
T Consensus 188 ~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v 254 (397)
T PRK14955 188 LEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL 254 (397)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence 4466777788888888889999999999999999987765 5455753 13467788887776
No 70
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=42.09 E-value=47 Score=22.41 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=31.4
Q ss_pred hcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023705 143 VNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (278)
Q Consensus 143 VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV 183 (278)
..-+..-++-|.++|..+ .-.+......|..++|-+...|
T Consensus 5 ~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 5 TRFTKEQLKVLEEYFQEN-PYPSKEEREELAKELGLTERQV 44 (57)
T ss_dssp SSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHHTSSHHHH
T ss_pred CCCCHHHHHHHHHHHHHh-cccccccccccccccccccccc
Confidence 345667778888899884 4488888889999999888887
No 71
>PHA02902 putative IMV membrane protein; Provisional
Probab=41.77 E-value=22 Score=28.10 Aligned_cols=54 Identities=24% Similarity=0.320 Sum_probs=35.2
Q ss_pred HHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhc---CCCCCCchHHHHHHH
Q 023705 109 ILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQK---GGDAVNPPALKGLVQ 174 (278)
Q Consensus 109 LlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~---gRdal~~gvLk~L~~ 174 (278)
|+|+-++.+- -++||.||-+|--.||+.+-+|. ++++++ =+|.++++-.|.|-+
T Consensus 8 i~~v~v~Ivc-lliya~YrR~kci~sP~~~d~~~-----------~~~l~~d~~F~D~lTpDQirAlHr 64 (70)
T PHA02902 8 ILAVIVIIFC-LLIYAAYKRYKCIPSPDDRDERF-----------GDTLEDDPLFKDSLTPDQIKALHR 64 (70)
T ss_pred HHHHHHHHHH-HHHHHHHHHhcCCCCCCCccccc-----------cccCCCCchhhccCCHHHHHHHHH
Confidence 5555555544 45566666655558888776653 566666 468888888887754
No 72
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=41.54 E-value=12 Score=24.72 Aligned_cols=23 Identities=17% Similarity=0.556 Sum_probs=18.9
Q ss_pred CChHHHHHHHHHHHhcCCCCChH
Q 023705 178 FSMEDVLRKYIRYALNEKPFNPD 200 (278)
Q Consensus 178 Fs~~EV~RKYirY~LnEr~F~pd 200 (278)
++..|++-+||.|.|..|-+..+
T Consensus 3 ~~nR~lV~~yi~yKLsQrgy~w~ 25 (27)
T PF02180_consen 3 YDNRELVEDYISYKLSQRGYVWE 25 (27)
T ss_dssp HHHHHHHHHHHHHHHHHTTSTST
T ss_pred ccHHHHHHHHHHHHhhhcCCCCC
Confidence 56789999999999998876543
No 73
>PHA01976 helix-turn-helix protein
Probab=41.01 E-value=19 Score=24.93 Aligned_cols=30 Identities=13% Similarity=0.336 Sum_probs=21.6
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023705 203 VNLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (278)
Q Consensus 203 aDLi~Lrkas~L~D~evaEiLnE~srRiv~~ 233 (278)
.-|.++|+..|||-.|+|+.+. +++.-+.+
T Consensus 5 ~rl~~~R~~~glt~~~lA~~~g-vs~~~v~~ 34 (67)
T PHA01976 5 IQLIKARNARAWSAPELSRRAG-VRHSLIYD 34 (67)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC-CCHHHHHH
Confidence 3467888999999999998886 44444433
No 74
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=40.57 E-value=98 Score=24.83 Aligned_cols=55 Identities=18% Similarity=0.326 Sum_probs=34.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH-hc--------CCCCChHHHHHHHHHH--hhcCCCcHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYA-LN--------EKPFNPDLVVNLIQLR--KASMLDDSQVAEILN 224 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~-Ln--------Er~F~pd~VaDLi~Lr--kas~L~D~evaEiLn 224 (278)
+.++.+++|-|..-| |-|-+=- |. -|-|+++.+..|-.++ +.+|++-+||+++|.
T Consensus 2 I~e~a~~~gvs~~tl-R~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~ 67 (124)
T TIGR02051 2 IGELAKAAGVNVETI-RYYERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLG 67 (124)
T ss_pred HHHHHHHHCcCHHHH-HHHHHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 346677777777655 7774422 21 2337777777665444 567888888888775
No 75
>PRK10026 arsenate reductase; Provisional
Probab=39.34 E-value=43 Score=28.45 Aligned_cols=80 Identities=28% Similarity=0.423 Sum_probs=48.5
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHH----HHHHHhcCCCCChHHHHHHHH--------------HHhhcCCCcHHHHHH
Q 023705 161 GDAVNPPALKGLVQKTGFSMEDVLRK----YIRYALNEKPFNPDLVVNLIQ--------------LRKASMLDDSQVAEI 222 (278)
Q Consensus 161 Rdal~~gvLk~L~~KTGFs~~EV~RK----YirY~LnEr~F~pd~VaDLi~--------------Lrkas~L~D~evaEi 222 (278)
.+.++...|+.+-.++|.+..+++|+ |=.-.+.+...+.+.+.++|+ -+...|=..+.|.++
T Consensus 36 ~~ppt~~eL~~~l~~~g~~~~~lint~~~~yr~L~~~~~~ls~~e~l~ll~~~P~LIKRPIi~~~~~a~i~Rp~e~v~~~ 115 (141)
T PRK10026 36 ETPPTRDELVKLIADMGISVRALLRKNVEPYEELGLAEDKFTDDQLIDFMLQHPILINRPIVVTPLGTRLCRPSEVVLEI 115 (141)
T ss_pred CCCcCHHHHHHHHHhCCCCHHHHHHcCCchHHHcCCCccCCCHHHHHHHHHhCccceeCcEEEcCCCeEEECCHHHHHHH
Confidence 57789999999999999999999986 332233334455454444443 134455566677777
Q ss_pred HHHHHHh--hhhhcCcccccc
Q 023705 223 LNEISRR--FVREKDEDALDE 241 (278)
Q Consensus 223 LnE~srR--iv~~~G~vmmn~ 241 (278)
|. .+.| +|++-|.+.+|-
T Consensus 116 l~-~~~~~~~~~~~~~~~~~~ 135 (141)
T PRK10026 116 LP-DAQKGAFTKEDGEKVVDE 135 (141)
T ss_pred hc-ccccccccccCCeEeecC
Confidence 72 2222 344444444443
No 76
>PF02797 Chal_sti_synt_C: Chalcone and stilbene synthases, C-terminal domain; InterPro: IPR012328 Synonym(s): Chalcone synthase, Flavonone synthase, 6'-deoxychalcone synthase Naringenin-chalcone synthases (2.3.1.74 from EC) and stilbene synthases (STS) (formerly known as resveratrol synthases) are related plant enzymes. CHS is an important enzyme in flavanoid biosynthesis and STS is a key enzyme in stilbene-type phyloalexin biosynthesis. Both enzymes catalyze the addition of three molecules of malonyl-CoA to a starter CoA ester (a typical example is 4-coumaroyl-CoA), producing either a chalcone (with CHS) or stilbene (with STS) []. These enzymes have a conserved cysteine residue, located in the central section of the protein sequence, which is essential for the catalytic activity of both enzymes and probably represents the binding site for the 4-coumaryl-CoA group []. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 3OV2_A 3OV3_B 1Z1F_A 1Z1E_A 3ALE_C 3OIT_A 2H84_A 1TEE_D 1TED_A 2P0U_A ....
Probab=39.22 E-value=22 Score=30.09 Aligned_cols=35 Identities=26% Similarity=0.190 Sum_probs=24.2
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCcc
Q 023705 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDED 237 (278)
Q Consensus 198 ~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~v 237 (278)
-|+==+=|-++.++++|+++++ +-||.++++||+.
T Consensus 66 HPGG~~ILd~v~~~L~L~~~~l-----~~Sr~vLr~yGNm 100 (151)
T PF02797_consen 66 HPGGRKILDAVEEALGLSPEQL-----RASREVLREYGNM 100 (151)
T ss_dssp E-SSHHHHHHHHHHHTS-GGGG-----HHHHHHHHHH-B-
T ss_pred cCChHHHHHHHHHHcCCCHHHH-----HHHHHHHHhcCCC
Confidence 3444455667889999999986 4699999999963
No 77
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=38.85 E-value=11 Score=31.34 Aligned_cols=9 Identities=33% Similarity=0.549 Sum_probs=5.2
Q ss_pred HHHHhcchh
Q 023705 69 VEVEEELPW 77 (278)
Q Consensus 69 ~e~e~e~~w 77 (278)
||+|++|.|
T Consensus 100 ee~ddDmgf 108 (112)
T PTZ00373 100 EEEEDDLGF 108 (112)
T ss_pred ccccccccc
Confidence 444556765
No 78
>PRK07668 hypothetical protein; Validated
Probab=38.77 E-value=45 Score=31.11 Aligned_cols=48 Identities=10% Similarity=0.284 Sum_probs=34.8
Q ss_pred ChHHHHHH-HHHHhhcCCCcHHHHHHHHHHHHhhhhh--cCccccccchhhhhhcccCC
Q 023705 198 NPDLVVNL-IQLRKASMLDDSQVAEILNEISRRFVRE--KDEDALDEQPPMQALFVFDP 253 (278)
Q Consensus 198 ~pd~VaDL-i~Lrkas~L~D~evaEiLnE~srRiv~~--~G~vmmn~~~avqalf~~~~ 253 (278)
|+|.+.|| .+| ...|++|+|+.|+|+|+-..+.+. .|. -..-+||+||
T Consensus 6 Neefl~~L~~yL-~~~glseeeieeiL~Ei~~hLlEgQk~Gk-------TA~~IfG~sP 56 (254)
T PRK07668 6 GRKFLDDTRVYL-IAKGIKEEDIESFLEDAELHLIEGEKDGK-------TVEDIFGDSP 56 (254)
T ss_pred HHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHcCC-------cHHHHhCCCH
Confidence 56778887 456 456899999999999999988753 342 2344677665
No 79
>PHA00739 V3 structural protein VP3
Probab=38.65 E-value=21 Score=29.38 Aligned_cols=35 Identities=34% Similarity=0.534 Sum_probs=27.6
Q ss_pred hcccccccc--CCC-cCCCCCchhHHhhhhHhhhhhhh
Q 023705 88 FTGSVTQAI--PGP-RVGQSKLPWILAVPLAYVGVSFV 122 (278)
Q Consensus 88 ftG~vtQAI--PGP-RVg~s~lPwLlAlPLAylG~TFv 122 (278)
.+|++||.- |.| -||+|..|.+--+|++|+=+-.+
T Consensus 42 vsgt~ttssfv~np~Yvgssnat~~sLVPlFYllVlIi 79 (92)
T PHA00739 42 VSGTVTTSSFVSNPQYVGSSNATLVSLVPLFYLLVLII 79 (92)
T ss_pred EeeeEEeeccccCcceecCCCCchHhHHHHHHHHHHHH
Confidence 457777664 888 69999999999999999864443
No 80
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=38.56 E-value=11 Score=31.19 Aligned_cols=12 Identities=17% Similarity=0.459 Sum_probs=6.7
Q ss_pred hhhHHHHhcchh
Q 023705 66 EVEVEVEEELPW 77 (278)
Q Consensus 66 e~e~e~e~e~~w 77 (278)
|+|||+|++|.|
T Consensus 98 e~eeE~ddDmGf 109 (113)
T PLN00138 98 EEKEESDDDMGF 109 (113)
T ss_pred cccccccccccc
Confidence 334455667765
No 81
>PHA02591 hypothetical protein; Provisional
Probab=38.34 E-value=26 Score=28.47 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=27.6
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023705 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (278)
Q Consensus 198 ~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~ 234 (278)
+.|.+..|.+-=...|||-+|||+.|. ++++.|++|
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~LG-VsqetVrKY 79 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASLLG-VSVRKVRRY 79 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHH
Confidence 456677777766788999999999874 677777776
No 82
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=38.27 E-value=36 Score=28.52 Aligned_cols=30 Identities=17% Similarity=0.164 Sum_probs=22.4
Q ss_pred HHHhhcCCCcHHHHHHH---HHHHHhhhhhcCc
Q 023705 207 QLRKASMLDDSQVAEIL---NEISRRFVREKDE 236 (278)
Q Consensus 207 ~Lrkas~L~D~evaEiL---nE~srRiv~~~G~ 236 (278)
.-+..-|.|++|+-+-| +|+|+.+..+|+-
T Consensus 34 ~d~~~~G~sEeeii~~LG~P~~iA~~i~~~~~i 66 (181)
T PF08006_consen 34 DDAGEEGKSEEEIIAELGSPKEIAREILAEYSI 66 (181)
T ss_pred HHhhhCCCCHHHHHHHcCCHHHHHHHHHHhhhh
Confidence 34556788888888877 7888888888763
No 83
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=37.96 E-value=10 Score=36.26 Aligned_cols=12 Identities=25% Similarity=0.255 Sum_probs=6.3
Q ss_pred hhhHHHHhcchh
Q 023705 66 EVEVEVEEELPW 77 (278)
Q Consensus 66 e~e~e~e~e~~w 77 (278)
|+|||+|++|..
T Consensus 308 ~~~e~~~~d~~~ 319 (323)
T PTZ00240 308 EEEESDEDDFGM 319 (323)
T ss_pred CCccCcccccCc
Confidence 444555566643
No 84
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=37.89 E-value=2.1e+02 Score=26.13 Aligned_cols=59 Identities=14% Similarity=0.188 Sum_probs=44.5
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
..+.+-|.+.+.+.+-.++..++..|...+|-|+..+ +.|..-|+-.+ -+.+.|.+++.
T Consensus 170 ~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~--it~~~v~~~~~ 231 (367)
T PRK14970 170 KDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN--ITRQAVTENLN 231 (367)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC--CCHHHHHHHhC
Confidence 4567778888888777899999999999999988755 56666675433 67776666653
No 85
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=37.76 E-value=40 Score=29.82 Aligned_cols=40 Identities=20% Similarity=0.197 Sum_probs=33.0
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH-------------HhhhhhcC
Q 023705 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS-------------RRFVREKD 235 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s-------------rRiv~~~G 235 (278)
.+++|.|.|+|-==.--|++.|||+-+|++-- -||.++.|
T Consensus 24 ~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk~~G 76 (148)
T PTZ00072 24 KLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILKKNG 76 (148)
T ss_pred cCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHHhcC
Confidence 46888999888666667999999999999764 57888888
No 86
>PRK09726 antitoxin HipB; Provisional
Probab=37.64 E-value=42 Score=25.27 Aligned_cols=38 Identities=16% Similarity=0.315 Sum_probs=28.3
Q ss_pred CCCChHHHH-HHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023705 195 KPFNPDLVV-NLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (278)
Q Consensus 195 r~F~pd~Va-DLi~Lrkas~L~D~evaEiLnE~srRiv~~ 233 (278)
..+++..+. .|-.+|+..|+|.+|+|+.+. +++.-+.+
T Consensus 6 ~~~~~~~l~~~lk~~R~~~gltq~elA~~~g-vs~~tis~ 44 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIG-IKQATISN 44 (88)
T ss_pred cccCHHHHHHHHHHHHHHcCCCHHHHHHHHC-cCHHHHHH
Confidence 567777775 456789999999999999887 55554444
No 87
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=37.56 E-value=1.2e+02 Score=24.07 Aligned_cols=67 Identities=15% Similarity=0.241 Sum_probs=38.5
Q ss_pred HHHHHHHhCCC---hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCcccccc
Q 023705 169 LKGLVQKTGFS---MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDE 241 (278)
Q Consensus 169 Lk~L~~KTGFs---~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~ 241 (278)
.+.|..+.||. +.+|+|+++. .+.+. -..+.++++ ....+.+..+.+.|.+.......+.+.+++|-
T Consensus 20 ~~~l~~~~g~~~~~~g~~~~~~~~---~~~~~-~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~~~i~dg 89 (188)
T TIGR01360 20 CEKIVEKYGFTHLSTGDLLRAEVA---SGSER-GKQLQAIME--SGDLVPLDTVLDLLKDAMVAALGTSKGFLIDG 89 (188)
T ss_pred HHHHHHHhCCcEEeHHHHHHHHHh---cCCHH-HHHHHHHHH--CCCCCCHHHHHHHHHHHHHcccCcCCeEEEeC
Confidence 45677777764 7788888653 12221 123444432 34455666777777776655555555677764
No 88
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=37.42 E-value=2e+02 Score=29.70 Aligned_cols=60 Identities=20% Similarity=0.264 Sum_probs=45.7
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHh---cCCCCChHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYAL---NEKPFNPDLVVNLI 206 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~L---nEr~F~pd~VaDLi 206 (278)
..+.+-|.+.+.+++-.++..++..|...+|-|+..+++ |=+-|.. ..+.-+.+.|.+++
T Consensus 189 ~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv 254 (620)
T PRK14954 189 DEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELL 254 (620)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhccccccCCccCHHHHHHHH
Confidence 445666777777777779999999999999999987765 5566763 25567777787765
No 89
>PF06595 BDV_P24: Borna disease virus P24 protein; InterPro: IPR009517 Borna disease virus (BDV) is a non-cytolytic, neurotropic RNA virus that has a broad host range in warm-blooded animals. BDV is an enveloped virus, non-segmented, negative-stranded RNA genome and has an organisation characteristic of a member of Bornaviridae in the order of Mononegavirale. This family consists of several BDV P24 (phosphoprotein 24) proteins. They are essential components of the RNA polymerase transcription and replication complex. P24 is encoded by open reading frame II (ORF-II) and undergoes high rates of mutation in humans. They bind amphoterin-HMGB1, a multifunctional protein, directly may cause deleterious effects in cellular functions by its interference with HMGB1 []. Horse and human P24 have no species-specific amino acid residues, suggesting that the two viruses related [, ]. Numerous interactions of the immune system with the central nervous system have been described. Mood and psychotic disorders, such as severe depression and schizophrenia, are both heterogeneous disorders regarding clinical symptomatology, the acuity of symptoms, the clinical course and the treatment response []. BDV p24 RNA has been detected in the peripheral blood mononuclear cells (PBMCs) of psychiatric patients with such conditions []. Some studies find a significant difference in the prevalence of BDV p24 RNA in patients with mood disorders and schizophrenia [], whilst others find no difference between patients and control groups []. Consequently, debate about the role of BDV in psychiatric diseases remains alive.
Probab=37.40 E-value=24 Score=32.30 Aligned_cols=81 Identities=21% Similarity=0.470 Sum_probs=48.0
Q ss_pred hcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhC---CChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023705 131 KFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTG---FSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 131 K~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTG---Fs~~EV~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
++.|| |+|.|.+|+.- -..++++.+-+. |++.+-.=.++|| .|.+|++++.+--
T Consensus 25 RSrSP---Rrrri~~~aLt-~pVe~Ll~~~kk--nPsmisD~~~~TGREqLSndeLikqLvtE----------------- 81 (201)
T PF06595_consen 25 RSRSP---RRRRIPRDALT-QPVEQLLKQLKK--NPSMISDPDQRTGREQLSNDELIKQLVTE----------------- 81 (201)
T ss_pred hcCCC---CcccCChHhhc-chHHHHHHHHhc--CCccccCCcccchHHhhchHHHHHHHHHH-----------------
Confidence 46778 33449998753 344444443221 3334444455666 4666766664432
Q ss_pred HHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023705 208 LRKASMLDDSQVAEILNEISRRFVREK 234 (278)
Q Consensus 208 Lrkas~L~D~evaEiLnE~srRiv~~~ 234 (278)
|-.-++.+-+.+...|.+++.||...+
T Consensus 82 lae~~mieaE~l~~~L~~i~~r~e~g~ 108 (201)
T PF06595_consen 82 LAENSMIEAEGLKGSLDDIAQRMESGL 108 (201)
T ss_pred HhhccchhHHHhhccHHHHHHHHHHhH
Confidence 234567777788888888998887654
No 90
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=37.21 E-value=2.3e+02 Score=23.09 Aligned_cols=110 Identities=19% Similarity=0.265 Sum_probs=61.3
Q ss_pred hhcCChhhhhhhhhcc--hhhHHhhHHHHHhcCCCCCCchHH-HHHH---HHhCCChHHHHHHHHHHHhcCCCCChHHHH
Q 023705 130 KKFNSPKFKRKKLVNK--NAMVCKTIDELFQKGGDAVNPPAL-KGLV---QKTGFSMEDVLRKYIRYALNEKPFNPDLVV 203 (278)
Q Consensus 130 rK~~SPraKRkR~VNK--NamLvkSLDeyFp~gRdal~~gvL-k~L~---~KTGFs~~EV~RKYirY~LnEr~F~pd~Va 203 (278)
++..|-+-=|.++..| +..+++..=+.|...+- +|...+ +... ...|++ +..|++.|..|-|+.+.+.
T Consensus 23 ~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~-ldD~~~a~~~~~~~~~~~~g-----~~~I~~~L~~kGi~~~~I~ 96 (157)
T PRK00117 23 RREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGL-LDDERFAESFVRSRARKGYG-----PRRIRQELRQKGVDREIIE 96 (157)
T ss_pred cchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCCch-----HHHHHHHHHHcCCCHHHHH
Confidence 3445555555566555 55566655555544332 332211 1111 123333 7789999999999999999
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCcc-ccccchhhhhhccc
Q 023705 204 NLIQLRKASMLDDSQVAEILNEISRRFVREKDED-ALDEQPPMQALFVF 251 (278)
Q Consensus 204 DLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~v-mmn~~~avqalf~~ 251 (278)
+.+.-- . .|++ |++.+.+++.++++-.. -....-+.|+|..|
T Consensus 97 ~~l~~~---~-~d~~--e~a~~~~~k~~~~~~~~~~~~k~Ki~~~L~rk 139 (157)
T PRK00117 97 EALAEL---D-IDWE--ELARELARKKFRRPLPDDAKEKAKLVRFLARR 139 (157)
T ss_pred HHHHHc---C-ccHH--HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC
Confidence 988742 2 3333 77777777777654221 01123556666544
No 91
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=37.09 E-value=50 Score=29.17 Aligned_cols=40 Identities=15% Similarity=0.238 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH-------------HhhhhhcC
Q 023705 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS-------------RRFVREKD 235 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s-------------rRiv~~~G 235 (278)
.+++|.|.++|-==.--|++.|||+-+|++.- -||.+++|
T Consensus 27 ~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~g 79 (151)
T PRK08561 27 DYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENG 79 (151)
T ss_pred cCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcC
Confidence 37889999988766667999999999999853 57777777
No 92
>COG2059 ChrA Chromate transport protein ChrA [Inorganic ion transport and metabolism]
Probab=37.00 E-value=30 Score=30.95 Aligned_cols=63 Identities=27% Similarity=0.478 Sum_probs=33.7
Q ss_pred hHHHHhcchhhHHh-hhhhhhhccccccccCCCc-------CCCCCchhHHhhhhH--hh--hhhhhhhhhhhhhhcCC
Q 023705 68 EVEVEEELPWIQEK-ALDLVEFTGSVTQAIPGPR-------VGQSKLPWILAVPLA--YV--GVSFVIAFVKTVKKFNS 134 (278)
Q Consensus 68 e~e~e~e~~wiqek-aldlveftG~vtQAIPGPR-------Vg~s~lPwLlAlPLA--yl--G~TFviA~vRtvrK~~S 134 (278)
++|..++-.||-|+ =.|++ ..+|.+|||- +|-.--.|.+|+-.. ++ ++-.++.+...+.+|.+
T Consensus 33 ~~e~V~~r~Wis~~ef~~~l----aisq~lPGP~a~~la~~vGy~~~G~~Ga~ia~lafvLPs~i~~~~l~~~~~~~~~ 107 (195)
T COG2059 33 RREVVERRKWISEEEFADAL----AISQLLPGPIATQLAIYVGYKLAGILGALIAGLAFVLPSILIMLGLALLLKRFGD 107 (195)
T ss_pred HHHHHHhccCCCHHHHHHHH----HHHhcCCCHHHHHHHHHHHHHHhchhHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 44555666999765 34444 3679999992 233333355555322 22 22233444555556653
No 93
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=36.85 E-value=62 Score=27.70 Aligned_cols=55 Identities=22% Similarity=0.329 Sum_probs=41.0
Q ss_pred CCchHHHHHHHHhCCChHHHHHHHHHHHhcCC--------CCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023705 164 VNPPALKGLVQKTGFSMEDVLRKYIRYALNEK--------PFNPDLVVNLIQLRKASMLDDSQVAEI 222 (278)
Q Consensus 164 l~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr--------~F~pd~VaDLi~Lrkas~L~D~evaEi 222 (278)
.....++.+..+.|.|..++. |+|+|... .-+++-|.+.++--.. -||++|+++|
T Consensus 216 ~~~~~l~~~a~~~g~s~~q~a---l~~~l~~~~~~~~i~g~~~~~~l~en~~a~~~-~L~~~~~~~i 278 (283)
T PF00248_consen 216 ELADALRELAEEHGVSPAQLA---LRWVLSHPGVASVIVGASSPEHLEENLAALDF-PLTEEELAEI 278 (283)
T ss_dssp GGHHHHHHHHHHHTSSHHHHH---HHHHHTSHTTEEEEEB-SSHHHHHHHHGGSSS-G--HHHHHHH
T ss_pred hhhhhhhhhhhhcccccchhh---hhhhhhccccccccCCCCCHHHHHHHHHHhCC-CCCHHHHHHH
Confidence 445689999999999999987 67777532 3678888888877644 9999999876
No 94
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=36.40 E-value=1.7e+02 Score=30.12 Aligned_cols=60 Identities=17% Similarity=0.198 Sum_probs=49.9
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
...+.+-|.+.+.+++-.++..+++.|.+.+|-|+.++ +.|.+-|. .+..|.+.|.+++.
T Consensus 193 ~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~g--~g~It~e~V~~llg 255 (598)
T PRK09111 193 ADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAHG--AGEVTAEAVRDMLG 255 (598)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhc--CCCcCHHHHHHHhC
Confidence 45778888888988888899999999999999998776 45778774 56789998888764
No 95
>PF06281 DUF1035: Protein of unknown function (DUF1035); InterPro: IPR009379 Sulfolobus virus-like particle SSV1 and its fusellovirus homologues can be found in many acidic (pH less than 4.0) hot springs (greater than 70 degrees C) around the world. SSV1 contains a 15.5-kb double-stranded DNA genome that encodes 34 proteins with greater than 50 amino acids []. A site-specific integrase and a DnaA-like protein have been previously identified by sequence homology, and three structural proteins have been isolated from purified virus and identified by N-terminal sequencing (VP1, VP2, and VP3).; GO: 0005198 structural molecule activity, 0016021 integral to membrane
Probab=36.20 E-value=28 Score=27.73 Aligned_cols=42 Identities=33% Similarity=0.515 Sum_probs=29.9
Q ss_pred ccccccc--cCCC-cCCCCCchhHHhhhhHhhhhhhhhhhhhhhh
Q 023705 89 TGSVTQA--IPGP-RVGQSKLPWILAVPLAYVGVSFVIAFVKTVK 130 (278)
Q Consensus 89 tG~vtQA--IPGP-RVg~s~lPwLlAlPLAylG~TFviA~vRtvr 130 (278)
.|++||. ++-| -+|+|..|.+--+|++|+=+..+.-.|-.+|
T Consensus 24 sgt~t~ssfv~nP~yvGSsnA~iv~LVplFylLvlIiVPAvi~Yk 68 (73)
T PF06281_consen 24 SGTVTTSSFVSNPQYVGSSNATIVSLVPLFYLLVLIIVPAVIAYK 68 (73)
T ss_pred ecceeeccccCCcceecCCCccHHHHHHHHHHHHHHHhhhheeee
Confidence 4777665 4778 6888899999999999996555443333333
No 96
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=35.86 E-value=19 Score=30.55 Aligned_cols=9 Identities=11% Similarity=0.505 Sum_probs=4.6
Q ss_pred HHHHhcchh
Q 023705 69 VEVEEELPW 77 (278)
Q Consensus 69 ~e~e~e~~w 77 (278)
||.+++|.+
T Consensus 100 eesddDmgf 108 (112)
T KOG3449|consen 100 EESDDDMGF 108 (112)
T ss_pred ccccccccc
Confidence 444555543
No 97
>PF00620 RhoGAP: RhoGAP domain; InterPro: IPR000198 Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large, multi-functional proteins []. A number of structure are known for this family [, , ]. The domain is composed of seven alpha helices. This domain is also known as the breakpoint cluster region-homology (BH) domain.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1RGP_A 1AM4_B 1GRN_B 2NGR_B 1OW3_A 1TX4_A 3BYI_B 1XA6_A 3FK2_B 1F7C_A ....
Probab=35.73 E-value=81 Score=24.55 Aligned_cols=57 Identities=14% Similarity=0.244 Sum_probs=34.1
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023705 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 145 KNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
-|..-++.|-+.|.+++..-. .+..-.=.+...++++|++= |.|--|+.+...++++
T Consensus 26 g~~~~~~~l~~~~~~~~~~~~-----~~~~~~~~~va~~lK~~L~~-lp~pli~~~~~~~~~~ 82 (151)
T PF00620_consen 26 GSSSEVQELRNKIDSGEPPNE-----NLENYDVHDVASLLKRFLRE-LPEPLIPSELYDKFIA 82 (151)
T ss_dssp --HHHHHHHHHHHHTTTTCST-----TGTTSTHHHHHHHHHHHHHH-SSSTSTTHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhhhcccc-----cccccChhhccccceeeeec-cccchhhhhHHHHHhh
Confidence 344445666666666655322 11122222345678888875 7888899988888885
No 98
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=35.71 E-value=76 Score=29.95 Aligned_cols=72 Identities=17% Similarity=0.293 Sum_probs=52.9
Q ss_pred HHHHHhCCChHHH--HHHHHHHHhcCC---CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH--hhhhhcCccccccc
Q 023705 171 GLVQKTGFSMEDV--LRKYIRYALNEK---PFNPDLVVNLIQLRKASMLDDSQVAEILNEISR--RFVREKDEDALDEQ 242 (278)
Q Consensus 171 ~L~~KTGFs~~EV--~RKYirY~LnEr---~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~sr--Riv~~~G~vmmn~~ 242 (278)
.=++.|||...|| |||-|...+-++ ...-++..|++-+++.-+|..+++.+.|..--+ -+++.-|-.-++..
T Consensus 86 ~SkmaT~f~~nEielfrkalE~im~sed~~~asst~~~~~vlq~k~k~L~ks~iE~lLqkf~q~gwf~e~eg~ftl~~r 164 (235)
T KOG4718|consen 86 DSKMATGFTANEIELFRKALEKIMSSEDCHIASSTAYNDIVLQAKSKPLKKSRIEELLQKFIQMGWFMEVEGRFTLGPR 164 (235)
T ss_pred hHHhcCCCCHHHHHHHHHHHHHHHhhhHhhhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhchhheecceEEEchH
Confidence 4468999999975 899998888772 123467788999999999999999999975443 23444555555544
No 99
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=35.71 E-value=1.9e+02 Score=22.66 Aligned_cols=8 Identities=38% Similarity=0.816 Sum_probs=3.3
Q ss_pred HhCCChHH
Q 023705 175 KTGFSMED 182 (278)
Q Consensus 175 KTGFs~~E 182 (278)
+.||+.+|
T Consensus 55 ~~G~sl~e 62 (123)
T cd04770 55 ALGFSLAE 62 (123)
T ss_pred HCCCCHHH
Confidence 34444444
No 100
>KOG2286 consensus Exocyst complex subunit SEC6 [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.62 E-value=66 Score=33.97 Aligned_cols=94 Identities=13% Similarity=0.199 Sum_probs=56.5
Q ss_pred hhhhhhhh-----hhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHh
Q 023705 118 GVSFVIAF-----VKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYAL 192 (278)
Q Consensus 118 G~TFviA~-----vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~L 192 (278)
|+++++.. =..+.|+.+++==-- +-=.-+|.++|+||+-=-.-+... +..+.... +.+++-+|||-++
T Consensus 481 ~~~~l~e~~~~d~~~~~~~lf~~~W~~g---~~~~~Iv~T~~dy~~D~~~~~~~~-f~~fi~e~---~~~~v~~Yl~~l~ 553 (667)
T KOG2286|consen 481 GVSGLLEEIFLDLQPLLNKLFTKEWCAG---SVTENIVATLDDYLPDFKELMGEY-FVRFIEEA---SLELVIEYLRALS 553 (667)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhch---hhHHHHHHHHHHHHHHHHHHhhhH-HHHHHHHH---HHHHHHHHHHHHH
Confidence 66666655 233444444332111 112348999999998644434444 33333332 4688999999999
Q ss_pred cCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH---HHHHhhhhhcCc
Q 023705 193 NEKPFNPDLVVNLIQLRKASMLDDSQVAEILN---EISRRFVREKDE 236 (278)
Q Consensus 193 nEr~F~pd~VaDLi~Lrkas~L~D~evaEiLn---E~srRiv~~~G~ 236 (278)
++|.++. |.+|-+. |+..++|++||.
T Consensus 554 ~kr~~~~------------------~~~~~i~~d~~~~~~~f~~~~~ 582 (667)
T KOG2286|consen 554 KKRASIQ------------------ELIEKIKSDAETLYHFFRKYGS 582 (667)
T ss_pred hhhhhHH------------------HHHHHHHhhHHHHHHHHHHhCc
Confidence 9999922 2222221 566889999999
No 101
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=35.47 E-value=11 Score=35.38 Aligned_cols=11 Identities=36% Similarity=0.465 Sum_probs=5.7
Q ss_pred hhhHHHHhcch
Q 023705 66 EVEVEVEEELP 76 (278)
Q Consensus 66 e~e~e~e~e~~ 76 (278)
|+|||+|++|.
T Consensus 295 ~~~ee~~~~~g 305 (310)
T PTZ00135 295 EEEEEEEDDMG 305 (310)
T ss_pred ccccCcchhcc
Confidence 44455555553
No 102
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=35.22 E-value=50 Score=25.85 Aligned_cols=54 Identities=19% Similarity=0.230 Sum_probs=42.5
Q ss_pred CChHHHHHH-HHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q 023705 178 FSMEDVLRK-YIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFV 231 (278)
Q Consensus 178 Fs~~EV~RK-YirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv 231 (278)
||.+||.+= .|+.+|++.-|+.+.+..++..........+++-..|+++-.-+.
T Consensus 39 Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (99)
T cd04765 39 YRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPSIRAELL 93 (99)
T ss_pred eCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHHHHHHHH
Confidence 788887763 466678899999999999999877777778888888887765543
No 103
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=34.66 E-value=89 Score=23.09 Aligned_cols=43 Identities=12% Similarity=0.306 Sum_probs=32.5
Q ss_pred HHHhcCCCCCCchHHHHHHHHhCCCh-HHHHHHHHHHHhcCCCCC
Q 023705 155 ELFQKGGDAVNPPALKGLVQKTGFSM-EDVLRKYIRYALNEKPFN 198 (278)
Q Consensus 155 eyFp~gRdal~~gvLk~L~~KTGFs~-~EV~RKYirY~LnEr~F~ 198 (278)
+++......+..+.|...-..+||+. ++-+|.+|++ |.+.-|+
T Consensus 5 ~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~-me~~Glt 48 (66)
T PF08461_consen 5 RILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRA-MERDGLT 48 (66)
T ss_pred HHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHH-HHHCCCc
Confidence 44555566788888888888889998 8999999998 4444454
No 104
>PRK04195 replication factor C large subunit; Provisional
Probab=34.59 E-value=2.1e+02 Score=27.71 Aligned_cols=90 Identities=18% Similarity=0.126 Sum_probs=0.0
Q ss_pred hHHhhhhHhhhhhhh----------hhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhC
Q 023705 108 WILAVPLAYVGVSFV----------IAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTG 177 (278)
Q Consensus 108 wLlAlPLAylG~TFv----------iA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTG 177 (278)
|-.+.-+...|+.+. +.+=..+++-+.-|.+|..+ ...+.+|.++++
T Consensus 304 ~~~~~~~m~~gv~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~-----------------------~~~~~~~~~~~~ 360 (482)
T PRK04195 304 WRYASDLMTAGVALAKEKKKRGFTRYQPPSYWRLLSKTKEKRETR-----------------------DSIAKKIAEKLH 360 (482)
T ss_pred HHHHHHHhhhHHHHhccccCCCCCCcCCcHHHHHHhhhhHHHHHH-----------------------HHHHHHHHHHhC
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 023705 178 FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEIL 223 (278)
Q Consensus 178 Fs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiL 223 (278)
-|...+-.-|+.|+.-=-.=| ...-++|-..++||++||.-++
T Consensus 361 ~s~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~ 403 (482)
T PRK04195 361 TSKRKVRREVLPFLSIIFKHN---PELAARLAAFLELTEEEIEFLT 403 (482)
T ss_pred CCHHHHHHHHHHHHHHHHhcC---HHHHHHHHHHcCCCHHHHHHHh
No 105
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=34.55 E-value=1.2e+02 Score=20.69 Aligned_cols=44 Identities=34% Similarity=0.403 Sum_probs=19.7
Q ss_pred HHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~ev 219 (278)
+.|.+++|.+.. .+.-.++.+.-++ .+..|.+|=++++.+-+|+
T Consensus 14 ~~La~~~gis~~-----tl~~~~~~~~~~~-~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 14 KDLARKTGISRS-----TLSRILNGKPSNP-SLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHT--HH-----HHHHHHTTT------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHHCcCHH-----HHHHHHhcccccc-cHHHHHHHHHHcCCCHHHH
Confidence 345555555543 3444556552222 2355666777777765553
No 106
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=34.34 E-value=1.9e+02 Score=22.99 Aligned_cols=10 Identities=10% Similarity=0.518 Sum_probs=5.2
Q ss_pred HHhCCChHHH
Q 023705 174 QKTGFSMEDV 183 (278)
Q Consensus 174 ~KTGFs~~EV 183 (278)
++.|||.+||
T Consensus 54 r~~G~sL~eI 63 (127)
T cd04784 54 RSLDMSLDEI 63 (127)
T ss_pred HHcCCCHHHH
Confidence 3455555554
No 107
>PRK06361 hypothetical protein; Provisional
Probab=34.14 E-value=55 Score=27.57 Aligned_cols=40 Identities=10% Similarity=0.090 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcC
Q 023705 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKD 235 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G 235 (278)
+-+.+....+.++.+-.|++++||-.++.+.-+|+.+.-|
T Consensus 173 ~~d~~~~~~~~~i~~~~gl~~~~v~~~~~~~~~~~~~~~~ 212 (212)
T PRK06361 173 PSDLITYEFARKVALGAGLTEKELEEALENNPKLLLKRLG 212 (212)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhHHHHHHhcC
Confidence 4455667888999999999999999999999999987655
No 108
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=33.88 E-value=2.2e+02 Score=21.92 Aligned_cols=95 Identities=15% Similarity=0.217 Sum_probs=50.8
Q ss_pred hhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCC-C--CchHHHHHHHHhCCChHHHHHHHHHHHhcC
Q 023705 118 GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDA-V--NPPALKGLVQKTGFSMEDVLRKYIRYALNE 194 (278)
Q Consensus 118 G~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRda-l--~~gvLk~L~~KTGFs~~EV~RKYirY~LnE 194 (278)
..+|+-+|.=|+|.|+||.. |++.|-+.|..--.. . .....+.++.+ ...|++..+..--.
T Consensus 25 d~~f~~~Flltyr~F~tp~~-----------ll~~L~~rf~~~~~~~~~~~~~~~~~~~~r----v~~~l~~Wv~~~~~- 88 (127)
T smart00229 25 DPFFVETFLLTYRSFITTQE-----------LLQLLLYRYNAIPPESWVERKVNPLRVKNR----VLNILRHWVENYWQ- 88 (127)
T ss_pred CHHHHHHHHHHhhhhCCHHH-----------HHHHHHHHhCCCCcHHHHHHHhhHHHHHHH----HHHHHHHHHHHCCc-
Confidence 45788888889999999983 555555555542221 0 01111122222 35566666655443
Q ss_pred CCCChH--HHHHHHHHHhhcCCC-cHHHHHHHHHHHHh
Q 023705 195 KPFNPD--LVVNLIQLRKASMLD-DSQVAEILNEISRR 229 (278)
Q Consensus 195 r~F~pd--~VaDLi~Lrkas~L~-D~evaEiLnE~srR 229 (278)
-|+.+ ....|..+-....-+ ..+..+-|.++.++
T Consensus 89 -dF~~~~~l~~~l~~f~~~~~~~~~~~~~~~l~~~~~~ 125 (127)
T smart00229 89 -DFEDDPKLILRLLEFLDLVDQEKGPGLVTSLQELLQR 125 (127)
T ss_pred -ccccCHHHHHHHHHHHHHHhhCcCCCHHHHHHHHHHh
Confidence 46655 555565555443333 34445555555554
No 109
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=33.63 E-value=17 Score=29.86 Aligned_cols=7 Identities=0% Similarity=0.567 Sum_probs=4.3
Q ss_pred HHhcchh
Q 023705 71 VEEELPW 77 (278)
Q Consensus 71 ~e~e~~w 77 (278)
.|++|.|
T Consensus 99 ~ddDmGf 105 (109)
T cd05833 99 SDDDMGF 105 (109)
T ss_pred cccccCC
Confidence 4566765
No 110
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=33.53 E-value=2.2e+02 Score=22.07 Aligned_cols=83 Identities=23% Similarity=0.332 Sum_probs=42.5
Q ss_pred hhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHH---hCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCC
Q 023705 139 RKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQK---TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLD 215 (278)
Q Consensus 139 RkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~K---TGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~ 215 (278)
+...-|.|.+.-++++ |+.+-..--+...++.+.+. .|.+..|++ =.+|=+|-+.+.+--+|.== ...++
T Consensus 30 ~~~~~~~~~~~~~~~~-Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~-----qi~Nl~P~~~~El~~ii~~~-~~r~~ 102 (117)
T PF03874_consen 30 EDPPENLNTIQYKTLE-YLEKFSKFQNPESIKELREELKKFGLTEFEIL-----QIINLRPTTAVELRAIIESL-ESRFS 102 (117)
T ss_dssp HHCSSCHCHHHHHHHH-HHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHH-----HHHHH--SSHHHHHHHSTTG-TTTST
T ss_pred cccccchHHHHHHHHH-HHHccccCCCHHHHHHHHHHHhcccCCHHHHH-----HHhcCCCCCHHHHHHHHHHh-ccCCC
Confidence 3344455666666666 77663333334444444333 344444433 24555555554444433211 12589
Q ss_pred cHHHHHHHHHHHH
Q 023705 216 DSQVAEILNEISR 228 (278)
Q Consensus 216 D~evaEiLnE~sr 228 (278)
|+++.+||..++.
T Consensus 103 ee~l~~iL~~v~~ 115 (117)
T PF03874_consen 103 EEDLEEILDLVSK 115 (117)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988764
No 111
>COG4858 Uncharacterized membrane-bound protein conserved in bacteria [Function unknown]
Probab=33.40 E-value=72 Score=29.88 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=22.9
Q ss_pred hcCCCcHHHHHHHHHHHHhhhh--hcCcc
Q 023705 211 ASMLDDSQVAEILNEISRRFVR--EKDED 237 (278)
Q Consensus 211 as~L~D~evaEiLnE~srRiv~--~~G~v 237 (278)
.-|-||+|+.+||+|+-..|.+ |+|..
T Consensus 33 ~~gksdeeik~Il~e~ipqIleeQkkGit 61 (226)
T COG4858 33 GDGKSDEEIKIILEEMIPQILEEQKKGIT 61 (226)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHhhhccch
Confidence 4689999999999999999986 46654
No 112
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=33.17 E-value=1.8e+02 Score=28.38 Aligned_cols=106 Identities=16% Similarity=0.234 Sum_probs=58.9
Q ss_pred cCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCC
Q 023705 100 RVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFS 179 (278)
Q Consensus 100 RVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs 179 (278)
-.+.++.-|.+.+++...| |++++|+.||+|=-|..--... +|=...-+.||+.|-+ +.+-..+=
T Consensus 77 ~~~~~rwrdy~vmAvi~aG--i~y~~y~~~K~YV~P~~l~~~~-~k~e~~k~~Ld~~~~~------------~~~~~~~l 141 (300)
T KOG2629|consen 77 QNVLRRWRDYFVMAVILAG--IAYAAYRFVKSYVLPRFLGESK-DKLEADKRQLDDQFDK------------AAKSLNAL 141 (300)
T ss_pred ccchhhHHHHHHHHHHHhh--HHHHHHHHHHHHHHHHhhCccc-hhHHHHHHHHHHHHHH------------HHHHHHHH
Confidence 3455667788888877777 8999999999998775322111 0224444566666543 23333333
Q ss_pred hHHH--HHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023705 180 MEDV--LRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 180 ~~EV--~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~ 226 (278)
++|| +|+-+--..+ +.-.+|-+|+.++-+.+..+.++=.|+
T Consensus 142 ~~~va~v~q~~~~qq~------Els~~L~~l~~~~~~~s~~~~k~esei 184 (300)
T KOG2629|consen 142 MDEVAQVSQLLATQQS------ELSRALASLKNTLVQLSRNIEKLESEI 184 (300)
T ss_pred HHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence 3343 2222222222 445566677776665555554443333
No 113
>PRK03892 ribonuclease P protein component 3; Provisional
Probab=32.95 E-value=98 Score=28.84 Aligned_cols=65 Identities=14% Similarity=0.133 Sum_probs=50.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCC--------------CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYALNEKP--------------FNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~LnEr~--------------F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~ 233 (278)
|+.|-+..|+...-+++.|-...-=-++ |+.-..-||++|=...|++.+|+.+.|.+..+.|.++
T Consensus 137 L~plL~~~G~~Rar~L~~~r~~l~L~rKYd~P~VISS~A~s~~~lRsPRdl~aL~~~iGme~~ea~~~Ls~~p~~i~~~ 215 (216)
T PRK03892 137 LSPLLRANPYERANILRFMMKAWQLVNKYKVPRFITSSAESKWEVRGPRDLMSLGINIGMEIPQAKASLSFYPRIILKR 215 (216)
T ss_pred cHHHHhhCchhHHHHHHHHHHHHHHHHHcCCCEEEecCcchhccCCCHHHHHHHHHHhCCCHHHHHHHHHHhHHHHhhc
Confidence 4455667788888888777665443344 4556778999999999999999999999999888764
No 114
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=32.88 E-value=71 Score=25.41 Aligned_cols=54 Identities=13% Similarity=0.129 Sum_probs=40.1
Q ss_pred ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccc
Q 023705 179 SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDA 238 (278)
Q Consensus 179 s~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vm 238 (278)
....+||--+|.+-.=+|-+.+.+| .|+|.+.+||+.+|....---|++-|.|+
T Consensus 21 ~~~~L~r~LLr~LA~G~PVt~~~LA------~a~g~~~e~v~~~L~~~p~tEyD~~GrIV 74 (77)
T PF12324_consen 21 GFAWLLRPLLRLLAKGQPVTVEQLA------AALGWPVEEVRAALAAMPDTEYDDQGRIV 74 (77)
T ss_dssp THHHHHHHHHHHHTTTS-B-HHHHH------HHHT--HHHHHHHHHH-TTSEEETTSEEE
T ss_pred ccHHHHHHHHHHHHcCCCcCHHHHH------HHHCCCHHHHHHHHHhCCCceEcCCCCee
Confidence 5678899999998888888877655 58999999999999988777777777765
No 115
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=32.86 E-value=2.3e+02 Score=21.89 Aligned_cols=33 Identities=12% Similarity=0.375 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhcCCC--CChH
Q 023705 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKP--FNPD 200 (278)
Q Consensus 168 vLk~L~~KTGFs~~EV~RKYirY~LnEr~--F~pd 200 (278)
....+-.+.|.++.+.+|-+++|..+|+. |++.
T Consensus 16 ~a~~i~~~lGl~~s~ai~~fl~qvv~~~~lPF~~~ 50 (83)
T TIGR02384 16 EAYAVFEELGLTPSTAIRMFLKQVIREQGLPFDLR 50 (83)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcC
Confidence 34456688999999999999999999975 5443
No 116
>TIGR01856 hisJ_fam histidinol phosphate phosphatase HisJ family. This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.
Probab=32.66 E-value=1.5e+02 Score=26.16 Aligned_cols=79 Identities=14% Similarity=0.139 Sum_probs=48.5
Q ss_pred CchHHHHHHHHhCCChHHHHHHHHHH--HhcCCCCChHHHHHHHHHHhhcCC------CcHHHHHHHHHHHHhhhhhcCc
Q 023705 165 NPPALKGLVQKTGFSMEDVLRKYIRY--ALNEKPFNPDLVVNLIQLRKASML------DDSQVAEILNEISRRFVREKDE 236 (278)
Q Consensus 165 ~~gvLk~L~~KTGFs~~EV~RKYirY--~LnEr~F~pd~VaDLi~Lrkas~L------~D~evaEiLnE~srRiv~~~G~ 236 (278)
+.+.+.....+.|-+.+++++.|... .+-+..|++|.++-+=-.|+-... ++..+-+.+.++.+.+-+.-..
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~i~~~~~~dvlgH~Dli~~~~~~~~~~~~~~~~~~~~~~~il~~~~~~g~~ 200 (253)
T TIGR01856 121 DAEEFNEGLVSFYGNLEQAQRDYFESVYDSIQALFKPLVIGHIDLVQKFGPLFTDVSSFSDEVYELLQRILKLVASQGKA 200 (253)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCcccHhHHHHhCccccccccccHHHHHHHHHHHHHHHHcCCE
Confidence 34455554456677899999999877 334556778888744223322222 4455667777776666555445
Q ss_pred cccccch
Q 023705 237 DALDEQP 243 (278)
Q Consensus 237 vmmn~~~ 243 (278)
+=+|++.
T Consensus 201 lEiNt~g 207 (253)
T TIGR01856 201 LEFNTSG 207 (253)
T ss_pred EEEEcHh
Confidence 5588873
No 117
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=32.62 E-value=49 Score=24.62 Aligned_cols=23 Identities=26% Similarity=0.395 Sum_probs=13.1
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHH
Q 023705 202 VVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 202 VaDLi~Lrkas~L~D~evaEiLn 224 (278)
+..|.+++++.|||..|+|+.|.
T Consensus 20 ~~~i~~~~~~~~ltQ~e~A~~lg 42 (80)
T PF13744_consen 20 MAAIRELREERGLTQAELAERLG 42 (80)
T ss_dssp HHHHHHHHHCCT--HHHHHHHHT
T ss_pred HHHHHHHHHHcCCCHHHHHHHHC
Confidence 44466666666666666666664
No 118
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=32.48 E-value=62 Score=23.14 Aligned_cols=31 Identities=19% Similarity=0.365 Sum_probs=27.0
Q ss_pred CCChHHHHHHHHHHhhcCC-CcHHHHHHHHHH
Q 023705 196 PFNPDLVVNLIQLRKASML-DDSQVAEILNEI 226 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L-~D~evaEiLnE~ 226 (278)
+++|....-++=++...|+ ||.++.|.+++-
T Consensus 4 ~~~~~~ml~~ll~~~~~~~~S~r~l~~~l~~~ 35 (77)
T PF05598_consen 4 AYPPRMMLKALLLKYLFGLRSDRELEERLRDN 35 (77)
T ss_pred CCCHHHHHHHHHHHHHHhcchHHHHHhhHhhh
Confidence 6888888889999999999 999999988764
No 119
>COG5590 Uncharacterized conserved protein [Function unknown]
Probab=32.45 E-value=1.7e+02 Score=27.55 Aligned_cols=52 Identities=25% Similarity=0.384 Sum_probs=40.3
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCCh--------------HHHHHHHHH-HHhcC-CCCC
Q 023705 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSM--------------EDVLRKYIR-YALNE-KPFN 198 (278)
Q Consensus 145 KNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~--------------~EV~RKYir-Y~LnE-r~F~ 198 (278)
|-+-+++++-|+.|.++ .|-+.+-+=.+++||+. ...|--|.| |+|.+ ++|+
T Consensus 28 kk~~~l~~llelvP~~g--wnn~li~eal~a~Gys~~~s~ilfP~g~~eLi~f~~~~~d~~aL~~lk~~d 95 (229)
T COG5590 28 KKIVFLQSLLELVPFNG--WNNRLIVEALEALGYSKGYSLILFPEGPMELIKFLEVYLDAYALESLKNID 95 (229)
T ss_pred HHHHHHHHHHHhccccc--cchhHHHHHHHhcCcccchhhhcCCCCHHHHHHHHHHHhHHHHHhcCCccc
Confidence 34568899999999975 67888888889999997 345677888 88876 4455
No 120
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.37 E-value=1.2e+02 Score=23.93 Aligned_cols=74 Identities=12% Similarity=0.175 Sum_probs=41.7
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHH---HhhcCCCcHHHHHHHHHHH
Q 023705 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQL---RKASMLDDSQVAEILNEIS 227 (278)
Q Consensus 151 kSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~L---rkas~L~D~evaEiLnE~s 227 (278)
+.|..+|+.=-+.|.....+.|.++-|+|-.||-+- .+ +.+=|.|.+-.++.. |.+.+=|=..+.++|+.+.
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~i--~~---~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~~~ 78 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDVA--KA---NERVTREQLYQMLLTWVNKTGRKASVNTLLDALEAIG 78 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHHH--HH---HCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHcc
Confidence 456677777666677777777777777777777542 11 123335555555532 3333344445555555554
Q ss_pred Hh
Q 023705 228 RR 229 (278)
Q Consensus 228 rR 229 (278)
.|
T Consensus 79 ~~ 80 (96)
T cd08315 79 LR 80 (96)
T ss_pred cc
Confidence 33
No 121
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=32.23 E-value=1.1e+02 Score=31.67 Aligned_cols=63 Identities=17% Similarity=0.294 Sum_probs=44.7
Q ss_pred ChHHHHHHHHHHHhc-------CCCCChHHHHHHHHH--Hhh-----cCCCcHHHHHHHHHHHHhhhhhcCccccccc
Q 023705 179 SMEDVLRKYIRYALN-------EKPFNPDLVVNLIQL--RKA-----SMLDDSQVAEILNEISRRFVREKDEDALDEQ 242 (278)
Q Consensus 179 s~~EV~RKYirY~Ln-------Er~F~pd~VaDLi~L--rka-----s~L~D~evaEiLnE~srRiv~~~G~vmmn~~ 242 (278)
+..|..++|++|.-. -++|++++++.||.- |.| +-|...++++++++ +.-+.++.|.-.++-+
T Consensus 315 d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~-a~~~a~~~~~~~i~~~ 391 (637)
T PRK13765 315 DTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRV-AGDIARSEGAELTTAE 391 (637)
T ss_pred CCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHH-HHHHHHhhccceecHH
Confidence 357889999998653 358999999999963 333 34678899999999 5556666665444433
No 122
>PHA03211 serine/threonine kinase US3; Provisional
Probab=32.23 E-value=20 Score=34.44 Aligned_cols=36 Identities=14% Similarity=0.200 Sum_probs=22.5
Q ss_pred hhhhhHHHHhcchhhHHhhhhhhhhccccccccCCC
Q 023705 64 AEEVEVEVEEELPWIQEKALDLVEFTGSVTQAIPGP 99 (278)
Q Consensus 64 ~~e~e~e~e~e~~wiqekaldlveftG~vtQAIPGP 99 (278)
+.+.++..+.++.+-.+.+.|.-.-.+.+...+|.+
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 127 (461)
T PHA03211 92 EDDDDDDAPDDVAYPDEYAEDDFLPGDGAPDHDPAP 127 (461)
T ss_pred hccCCCCCccccCCCCCCCCcceecCCCCCCCCCCC
Confidence 444455555666777777777666666666666554
No 123
>PRK11172 dkgB 2,5-diketo-D-gluconate reductase B; Provisional
Probab=32.19 E-value=1.7e+02 Score=25.79 Aligned_cols=58 Identities=14% Similarity=0.257 Sum_probs=41.2
Q ss_pred CchHHHHHHHHhCCChHHHHHHHHHHHhcCC------CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023705 165 NPPALKGLVQKTGFSMEDVLRKYIRYALNEK------PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (278)
Q Consensus 165 ~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr------~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s 227 (278)
+.+.|+.+.++.|-|..++. |+|.|.-. .-+++-+.+-++.-. .-||++|+++| +++.
T Consensus 188 ~~~~l~~~a~~~~~s~aqva---l~w~l~~~~~~i~g~~~~~~l~~n~~~~~-~~L~~~~~~~i-~~~~ 251 (267)
T PRK11172 188 KDPVIARIAAKHNATPAQVI---LAWAMQLGYSVIPSSTKRENLASNLLAQD-LQLDAEDMAAI-AALD 251 (267)
T ss_pred CCHHHHHHHHHhCCCHHHHH---HHHHHhCCCEeecCCCCHHHHHHHHhhcC-CCcCHHHHHHH-hhhc
Confidence 45789999999999999987 56777642 356777776655432 46899998766 4443
No 124
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=31.89 E-value=1.3e+02 Score=24.82 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 023705 180 MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (278)
Q Consensus 180 ~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRi 230 (278)
.+|.+..=++|+-+.+-=+-- .+.=++.=+.=|||++||.|+|.+....-
T Consensus 2 Re~li~~A~~FL~~p~V~~sp-~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 2 REDLIEQAVKFLQDPKVRNSP-LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHHCTTTCCCS--HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHHhCCcccccCC-HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 466777777777777655444 45555555566999999999998865544
No 125
>PF08519 RFC1: Replication factor RFC1 C terminal domain; InterPro: IPR013725 This is the C-terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [, ]. ; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_A.
Probab=31.71 E-value=20 Score=30.54 Aligned_cols=69 Identities=20% Similarity=0.202 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHhc--CCCCCh---HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccchhhhhhcc
Q 023705 179 SMEDVLRKYIRYALN--EKPFNP---DLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQPPMQALFV 250 (278)
Q Consensus 179 s~~EV~RKYirY~Ln--Er~F~p---d~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~~avqalf~ 250 (278)
+..||...|+-++.. -+|.-. |.|.+.|.+-...+|+-+|+ |-|.|++ .....-..+-+...+|-+-|.
T Consensus 77 ~~~~v~~~Ylp~L~~~l~~pL~~~~~~~v~~vi~~Md~Y~Ltred~-d~i~el~--~~~~~~~~~~~i~tkvKaafT 150 (155)
T PF08519_consen 77 SKSEVRLDYLPLLRQKLTQPLIEQGKDGVDEVIDLMDEYGLTREDW-DNIMELS--KWPGKEDPLKKIDTKVKAAFT 150 (155)
T ss_dssp -----------------------------------------------------------------------------
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCcccHHHHHHHHHHhCCCHHHH-HHHHHhc--cCCCCcccccCCcHHHHHHHH
Confidence 345665566544332 122222 48999999999999999999 8888988 333333333344455554443
No 126
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=31.25 E-value=1.6e+02 Score=23.82 Aligned_cols=42 Identities=17% Similarity=0.184 Sum_probs=27.5
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHH
Q 023705 171 GLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (278)
Q Consensus 171 ~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~ev 219 (278)
+|.+++|-| +.||.-..|.+. +| -...|..|=++++++-+++
T Consensus 23 eLA~~~Gis-----~~~is~iE~g~~-~p-s~~~l~kIa~aL~v~~~~L 64 (120)
T PRK13890 23 ELSERSGVS-----ISFLSDLTTGKA-NP-SLKVMEAIADALETPLPLL 64 (120)
T ss_pred HHHHHHCcC-----HHHHHHHHcCCC-CC-CHHHHHHHHHHHCCCHHHH
Confidence 444444444 347777778775 66 4477888888999955544
No 127
>PLN03244 alpha-amylase; Provisional
Probab=31.08 E-value=28 Score=37.78 Aligned_cols=20 Identities=30% Similarity=0.255 Sum_probs=15.9
Q ss_pred cccccccccccCCCCCCCCC
Q 023705 5 ATSSFSSLQFLPRPKIPQPP 24 (278)
Q Consensus 5 ~~~~~~~~q~~~~p~~p~~~ 24 (278)
+|++.||+||+.-|.+|+.+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~ 20 (872)
T PLN03244 1 MTSLSLPTQFSCHPNASNLP 20 (872)
T ss_pred CcccccccceeecCCCCCCC
Confidence 47889999999888776653
No 128
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=30.98 E-value=2.5e+02 Score=22.55 Aligned_cols=9 Identities=44% Similarity=1.007 Sum_probs=4.7
Q ss_pred HhCCChHHH
Q 023705 175 KTGFSMEDV 183 (278)
Q Consensus 175 KTGFs~~EV 183 (278)
+.|||..||
T Consensus 55 ~~G~sL~eI 63 (127)
T cd01108 55 DLGFSLEEI 63 (127)
T ss_pred HcCCCHHHH
Confidence 455555554
No 129
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=30.97 E-value=45 Score=25.52 Aligned_cols=55 Identities=11% Similarity=-0.003 Sum_probs=42.8
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCcccc
Q 023705 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDAL 239 (278)
Q Consensus 185 RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmm 239 (278)
.|-++..+++..+=..+.+|==++=...|||++|...+++---++++.-=|..++
T Consensus 6 ~~~~~~~~~~~~~re~f~~dp~a~~~~~~Lt~eE~~al~~rD~~~L~~lG~~~~~ 60 (77)
T cd07321 6 EKLLEQLLVKPEVKERFKADPEAVLAEYGLTPEEKAALLARDVGALYVLGVNPML 60 (77)
T ss_pred HHHHHHHhcCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHcCCHHHHHHcCCCHHH
Confidence 6777888888777777788887888888999999998887777777665555443
No 130
>PF07395 Mig-14: Mig-14; InterPro: IPR009977 This family contains a number of bacterial mig-14 proteins (approximately 270 residues long). In Salmonella, mig-14 contributes to resistance to antimicrobial peptides, although the mechanism is not fully understood [].
Probab=30.81 E-value=79 Score=29.92 Aligned_cols=100 Identities=20% Similarity=0.324 Sum_probs=64.1
Q ss_pred hhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHH
Q 023705 123 IAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLV 202 (278)
Q Consensus 123 iA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~V 202 (278)
|+++|+--.| |.|.+++|. .-|.+|..+|++ +..-.-||.+|+.+=|+
T Consensus 98 iclaK~~e~f-SkKt~~~rr--------rElrkF~~~GG~---------v~~v~~~S~~Ela~iY~-------------- 145 (264)
T PF07395_consen 98 ICLAKGPESF-SKKTRKNRR--------RELRKFIEAGGS---------VRPVSEFSPEELADIYI-------------- 145 (264)
T ss_pred eeeEcCchhh-chHHHHHHH--------HHHHHHHHcCCE---------EEEHHHCCHHHHHHHHH--------------
Confidence 4566643333 444444433 235566666665 33345699999999885
Q ss_pred HHHHHHHhhcCCCc-HHHHHHHHHHHHhhhhhcCcccc-ccc-hhhhhhcccCCccchh
Q 023705 203 VNLIQLRKASMLDD-SQVAEILNEISRRFVREKDEDAL-DEQ-PPMQALFVFDPVHNIC 258 (278)
Q Consensus 203 aDLi~Lrkas~L~D-~evaEiLnE~srRiv~~~G~vmm-n~~-~avqalf~~~~~~~~~ 258 (278)
||.+.|-+....+ ++++|.+.+.=.=| +|.|++ |-+ -|+|-++-.+-.++||
T Consensus 146 -~Lf~~Rwg~~~~~~~~l~e~f~~Lr~~~---fG~vL~l~~~P~Aiqlv~k~es~~wv~ 200 (264)
T PF07395_consen 146 -DLFQKRWGFRCYGKEHLAEFFSELRHMI---FGSVLFLNGQPCAIQLVYKVESPKWVY 200 (264)
T ss_pred -HHHHHHhCCCCCcHHHHHHHHHHhHHhh---eeeEEEECCcceEEEEEEEecCCCeEE
Confidence 7888888877666 57777776665544 577664 333 7888888777666665
No 131
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=30.78 E-value=2.5e+02 Score=28.10 Aligned_cols=75 Identities=16% Similarity=0.202 Sum_probs=53.8
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEI 222 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEi 222 (278)
...+.+.|...+.+.+-.++.++++.|.+.+|-|+-+++. +-+-| ....-+.+.|.+++. ..+++++-++
T Consensus 180 ~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq~ia~--~~~~It~~~V~~~lg-----~~~~~~i~~l 252 (509)
T PRK14958 180 PLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAY--GNGKVLIADVKTMLG-----TIEPLLLFDI 252 (509)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc--CCCCcCHHHHHHHHC-----CCCHHHHHHH
Confidence 4567778888888888889999999999999999988755 55656 356678888777642 2444555555
Q ss_pred HHHHH
Q 023705 223 LNEIS 227 (278)
Q Consensus 223 LnE~s 227 (278)
++.++
T Consensus 253 l~al~ 257 (509)
T PRK14958 253 LEALA 257 (509)
T ss_pred HHHHH
Confidence 54443
No 132
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=30.53 E-value=85 Score=22.81 Aligned_cols=68 Identities=18% Similarity=0.319 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHHHh-hcCCCcHHHHHHHHHHHHhhhhhcCccccccchhhhhhcccC
Q 023705 181 EDVLRKYIRYALNEKPFNPDLVVNLIQLRK-ASMLDDSQVAEILNEISRRFVREKDEDALDEQPPMQALFVFD 252 (278)
Q Consensus 181 ~EV~RKYirY~LnEr~F~pd~VaDLi~Lrk-as~L~D~evaEiLnE~srRiv~~~G~vmmn~~~avqalf~~~ 252 (278)
.+||++|-. +....+.+...+-+.=.. -..+|++++.++++.-.... +.+..-.|++++-..-|++++
T Consensus 3 ~~if~~ys~---~~~~mt~~~f~~FL~~eQ~~~~~~~~~~~~li~~~~~~~-~~~~~~~lt~~gF~~fL~S~~ 71 (83)
T PF09279_consen 3 EEIFRKYSS---DKEYMTAEEFRRFLREEQGEPRLTDEQAKELIEKFEPDE-RNRQKGQLTLEGFTRFLFSDE 71 (83)
T ss_dssp HHHHHHHCT---TSSSEEHHHHHHHHHHTSS-TTSSHHHHHHHHHHHHHHH-HHHCTTEEEHHHHHHHHHSTT
T ss_pred HHHHHHHhC---CCCcCCHHHHHHHHHHHhccccCcHHHHHHHHHHHccch-hhcccCCcCHHHHHHHHCCCc
Confidence 456666522 455566665555543222 22457777777776643222 222336788888888888876
No 133
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=30.41 E-value=62 Score=24.59 Aligned_cols=34 Identities=26% Similarity=0.326 Sum_probs=18.8
Q ss_pred HHHHHhcC-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023705 187 YIRYALNE-KPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 187 YirY~LnE-r~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~ 226 (278)
.||-+|+| ++.+ +-.|+++++|+|.++.-+|-=.
T Consensus 12 ~Vw~~L~~~~~~s------~~el~k~~~l~~~~~~~AiGWL 46 (65)
T PF10771_consen 12 KVWQLLNENGEWS------VSELKKATGLSDKEVYLAIGWL 46 (65)
T ss_dssp HHHHHHCCSSSEE------HHHHHHHCT-SCHHHHHHHHHH
T ss_pred HHHHHHhhCCCcC------HHHHHHHhCcCHHHHHHHHHHH
Confidence 35666777 3332 2234577777777776665433
No 134
>cd01310 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.
Probab=30.40 E-value=82 Score=26.02 Aligned_cols=33 Identities=21% Similarity=0.376 Sum_probs=25.5
Q ss_pred hHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhh
Q 023705 199 PDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFV 231 (278)
Q Consensus 199 pd~VaDLi~-Lrkas~L~D~evaEiLnE~srRiv 231 (278)
|..+..++. |....||+++++.+++.+-++|++
T Consensus 217 ~~~~~~~~~~la~~~gl~~e~~~~~~~~N~~~ll 250 (251)
T cd01310 217 PAYVKHVAEKIAELKGISVEEVAEVTTENAKRLF 250 (251)
T ss_pred ChhHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 334444444 556799999999999999999986
No 135
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=30.38 E-value=1.3e+02 Score=23.42 Aligned_cols=54 Identities=26% Similarity=0.330 Sum_probs=44.0
Q ss_pred HHHHHHhC--CC-hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 170 KGLVQKTG--FS-MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 170 k~L~~KTG--Fs-~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
.-|-+||| |. ..+--+++|+=-|+| -|+.|..--.|..+.+-=+.|.++..-|+
T Consensus 3 ~yLN~~tg~~f~~~~~~~~~~I~aRl~e-G~t~edf~~VID~k~~~W~~~~~m~~YLR 59 (74)
T PF09524_consen 3 DYLNKKTGKKFKSNTKSTKKLIKARLNE-GYTLEDFKKVIDNKVAEWKGDPKMEKYLR 59 (74)
T ss_pred HHHHHHhcCccCCCcHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHCCCHHHHHhcC
Confidence 34556666 66 678889999999999 89999999999999998888888777665
No 136
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=30.11 E-value=31 Score=25.66 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=17.2
Q ss_pred HHHhcCCCCChHHHHHHHH
Q 023705 189 RYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 189 rY~LnEr~F~pd~VaDLi~ 207 (278)
+|+.+||..++++|..++.
T Consensus 1 ~YL~~~RgI~~~~v~~~~~ 19 (77)
T PF13154_consen 1 AYLTEERGIDPEIVDAFIN 19 (77)
T ss_pred CchhhhcCcCHHHHHHHHH
Confidence 4899999999999999887
No 137
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=30.04 E-value=1.4e+02 Score=22.88 Aligned_cols=46 Identities=22% Similarity=0.292 Sum_probs=33.0
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhc
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN 193 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~Ln 193 (278)
..|++|.|.++ ++|.+.+..+++.-....+....+-++.+++.+|.
T Consensus 8 ~~MI~eAI~~l--~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLk 53 (88)
T cd00073 8 SEMVTEAIKAL--KERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALK 53 (88)
T ss_pred HHHHHHHHHHc--CCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHH
Confidence 46889999887 56777788888777776655444667777776664
No 138
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=29.99 E-value=3.3e+02 Score=28.31 Aligned_cols=59 Identities=19% Similarity=0.283 Sum_probs=45.3
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDLi 206 (278)
+..+.+.|.+.+.+.+-.++..+|+.|.+.++-|+.+++. +.+-|. .+.-+.+.|.+++
T Consensus 185 ~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lLdq~ia~~--~~~It~~~V~~~L 246 (618)
T PRK14951 185 PETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTDQAIAFG--SGQLQEAAVRQML 246 (618)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--CCCcCHHHHHHHH
Confidence 4566777777777778889999999999999999988765 556663 5567777776655
No 139
>PRK11565 dkgA 2,5-diketo-D-gluconate reductase A; Provisional
Probab=29.92 E-value=1.8e+02 Score=25.81 Aligned_cols=55 Identities=20% Similarity=0.394 Sum_probs=39.5
Q ss_pred CCchHHHHHHHHhCCChHHHHHHHHHHHhcCC------CCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023705 164 VNPPALKGLVQKTGFSMEDVLRKYIRYALNEK------PFNPDLVVNLIQLRKASMLDDSQVAEI 222 (278)
Q Consensus 164 l~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr------~F~pd~VaDLi~Lrkas~L~D~evaEi 222 (278)
+....|+.+.++.|-|+.+|. |||.|.-. .-+++-+.|-++.-. ..||++|+++|
T Consensus 197 ~~~~~l~~ia~~~g~s~aq~a---L~w~l~~~~~~I~g~~~~~~i~~n~~a~~-~~Ls~~~~~~i 257 (275)
T PRK11565 197 FDQKVIRDLADKYGKTPAQIV---IRWHLDSGLVVIPKSVTPSRIAENFDVFD-FRLDKDELGEI 257 (275)
T ss_pred ccCHHHHHHHHHhCCCHHHHH---HHHHHcCCCEeeCCCCCHHHHHHHHhccC-CCcCHHHHHHH
Confidence 456789999999999999997 56667542 234566666555433 36999998876
No 140
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=29.78 E-value=83 Score=21.75 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=23.2
Q ss_pred hHHHHHHHHhCCChHHHHHHHHHHHhcC
Q 023705 167 PALKGLVQKTGFSMEDVLRKYIRYALNE 194 (278)
Q Consensus 167 gvLk~L~~KTGFs~~EV~RKYirY~LnE 194 (278)
..|+.|..+||-...+++|+=|.-.|.+
T Consensus 15 ~~L~~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 15 EKLKELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3577899999999999999988777654
No 141
>PF04510 DUF577: Family of unknown function (DUF577); InterPro: IPR007598 This is a family of Arabidopsis thaliana (Mouse-ear cress) proteins. Many of these members contain a repeated region.
Probab=29.75 E-value=1.2e+02 Score=27.38 Aligned_cols=84 Identities=20% Similarity=0.319 Sum_probs=50.6
Q ss_pred cccccCCCcCCCCCchhHHhhhhHhh-hhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCC-CCCchHH
Q 023705 92 VTQAIPGPRVGQSKLPWILAVPLAYV-GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGD-AVNPPAL 169 (278)
Q Consensus 92 vtQAIPGPRVg~s~lPwLlAlPLAyl-G~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRd-al~~gvL 169 (278)
+.+.+=.|+- ...==|+||+--|+- ||-+ .-+ .+....-+.++++ +++|+.|+..+|.+ ++--.+|
T Consensus 89 ~~~~L~~p~~-~d~~~W~LAl~~a~~~~Iql----~e~----~~~~~~vk~L~~~---mv~Sv~elV~~g~E~~~l~rgl 156 (174)
T PF04510_consen 89 ISKVLLPPEE-VDVEDWVLALTGAVCMAIQL----LES----SMRVDLVKELLPK---MVKSVKELVERGMEVGFLRRGL 156 (174)
T ss_pred HHHHcCCchh-ccHHHHHHHHHHHHHHHHHH----hcc----ccHHHHHHHHHHH---HHHHHHHHHHcccHHHHHHHHH
Confidence 4445545543 222349998865554 3222 211 2223445556665 89999999999998 7766666
Q ss_pred HHHHHHhCCChHHHHHHHHHHHhcC
Q 023705 170 KGLVQKTGFSMEDVLRKYIRYALNE 194 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYirY~LnE 194 (278)
+.++.. |-|.+-||.-||
T Consensus 157 ~~~e~~-------v~~~~~~y~~~~ 174 (174)
T PF04510_consen 157 RDFESF-------VSRQMNWYKTSE 174 (174)
T ss_pred HHHHHH-------HHHHHHHhhccC
Confidence 666543 446677776554
No 142
>cd01836 FeeA_FeeB_like SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it turn are loaded onto the acyl carrier protein FeeL. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=29.01 E-value=67 Score=25.65 Aligned_cols=39 Identities=31% Similarity=0.412 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhhhhhc-Cccccccchhh-hhhcccCCccc
Q 023705 218 QVAEILNEISRRFVREK-DEDALDEQPPM-QALFVFDPVHN 256 (278)
Q Consensus 218 evaEiLnE~srRiv~~~-G~vmmn~~~av-qalf~~~~~~~ 256 (278)
+..+.+|+.-+++.+++ |--.+|+.... ..+|..|.+|-
T Consensus 133 ~~~~~~n~~~~~~a~~~~~~~~id~~~~~~~~~~~~DglHp 173 (191)
T cd01836 133 RRARLLNRALERLASEAPRVTLLPATGPLFPALFASDGFHP 173 (191)
T ss_pred HHHHHHHHHHHHHHhcCCCeEEEecCCccchhhccCCCCCC
Confidence 44567899999999999 88888988544 56778888773
No 143
>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Probab=28.92 E-value=2.4e+02 Score=23.74 Aligned_cols=60 Identities=10% Similarity=0.042 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccc
Q 023705 182 DVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQ 242 (278)
Q Consensus 182 EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~ 242 (278)
+-++++++..++|.+++-=.++.+-.|+-.. -++.+..+.+.++.+.+-+...|+++=.+
T Consensus 93 ~~l~~~~~~~i~~~~~~~vVIDsls~l~~~~-~~~~~~r~~l~~l~~~lk~~~~tvll~s~ 152 (224)
T TIGR03880 93 NRIKNELPILIKELGASRVVIDPISLLETLF-DDDAERRTELFRFYSSLRETGVTTILTSE 152 (224)
T ss_pred HHHHHHHHHHHHHhCCCEEEEcChHHHhhhc-CCHHHHHHHHHHHHHHHHhCCCEEEEEEc
Confidence 3467788888988887755555666664332 24566677778888877666666665443
No 144
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.71 E-value=1.8e+02 Score=22.57 Aligned_cols=55 Identities=16% Similarity=0.243 Sum_probs=0.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh--------cCCCCChHHHHHHHHHH--hh-cCCCcHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYAL--------NEKPFNPDLVVNLIQLR--KA-SMLDDSQVAEILN 224 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~L--------nEr~F~pd~VaDLi~Lr--ka-s~L~D~evaEiLn 224 (278)
+.++.+.+|-|. ..+|.|.++-| +-+-|+++.|+.|-.++ +. +|++-++|+++|.
T Consensus 4 i~eva~~~gVs~-~tLR~ye~~Gli~p~r~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~ 69 (98)
T cd01279 4 ISVAAELLGIHP-QTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIE 69 (98)
T ss_pred HHHHHHHHCcCH-HHHHHHHHCCCCCCCcCCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
No 145
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=28.51 E-value=1.6e+02 Score=21.11 Aligned_cols=22 Identities=27% Similarity=0.333 Sum_probs=18.4
Q ss_pred hcCCCcHHHHHHHHHHHHhhhh
Q 023705 211 ASMLDDSQVAEILNEISRRFVR 232 (278)
Q Consensus 211 as~L~D~evaEiLnE~srRiv~ 232 (278)
.-.|+++||..|.+-++++.++
T Consensus 50 ~~PL~~~Ev~~i~kSi~k~~~r 71 (71)
T PF08708_consen 50 SPPLPESEVKAIAKSIAKWTWR 71 (71)
T ss_pred CCCCCHHHHHHHHHHHHHhccC
Confidence 5679999999999999887653
No 146
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.37 E-value=2.8e+02 Score=22.26 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=5.4
Q ss_pred CCCCChHHHHHHHH
Q 023705 194 EKPFNPDLVVNLIQ 207 (278)
Q Consensus 194 Er~F~pd~VaDLi~ 207 (278)
+--|+.+.+.++++
T Consensus 55 ~~G~sL~eI~~~l~ 68 (126)
T cd04785 55 DLGFSLEEIRALLA 68 (126)
T ss_pred HCCCCHHHHHHHHh
Confidence 33333333333333
No 147
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=28.32 E-value=89 Score=27.32 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=28.3
Q ss_pred CChHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhhh
Q 023705 197 FNPDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFVR 232 (278)
Q Consensus 197 F~pd~VaDLi~-Lrkas~L~D~evaEiLnE~srRiv~ 232 (278)
-.|..+.+.++ |-+.-+++.+|+++++.+-++|+|.
T Consensus 219 ~~p~~i~~~~~~la~~~~~~~e~~~~~~~~N~~r~f~ 255 (255)
T PF01026_consen 219 NEPSNIPKVAQALAEIKGISLEELAQIIYENAKRLFG 255 (255)
T ss_dssp --GGGHHHHHHHHHHHHTSTHHHHHHHHHHHHHHHHT
T ss_pred CChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhC
Confidence 36777776665 6667789999999999999999983
No 148
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=28.30 E-value=2.8e+02 Score=22.60 Aligned_cols=45 Identities=20% Similarity=0.404 Sum_probs=23.7
Q ss_pred CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH------HhhhhhcCcccc
Q 023705 195 KPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS------RRFVREKDEDAL 239 (278)
Q Consensus 195 r~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s------rRiv~~~G~vmm 239 (278)
-+++|+.+++||+|=..=.+|...+.++|.+.. +-+++++|-..+
T Consensus 38 ~~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~~~~~~~~~ii~~~~l~~i 88 (148)
T PF02637_consen 38 SPISPEHLAELINLLEDGKISKKSAKELLRELLENGKSPEEIIEENGLWQI 88 (148)
T ss_dssp SSSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTS-HHHHHHHTT---B
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCcC
Confidence 356666666666666555666666666665543 234455554444
No 149
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=28.17 E-value=1.1e+02 Score=24.04 Aligned_cols=42 Identities=17% Similarity=0.305 Sum_probs=25.4
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023705 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (278)
Q Consensus 185 RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~ 234 (278)
+++|+..|..|-.+++.+++.+. ..++.+. +.+++++-++.+
T Consensus 45 ~~~I~~~L~~kGi~~~~i~~~l~-----~~~~~e~---a~~~~~kk~~~~ 86 (121)
T PF02631_consen 45 PRRIRQKLKQKGIDREIIEEALE-----EYDEEEE---ALELAEKKYRRY 86 (121)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHT-----CS-HHHH---HHHHHHHHHHHT
T ss_pred HHHHHHHHHHHCCChHHHHHHHH-----HhhHHHH---HHHHHHHHHhcc
Confidence 46777777888888887777766 3333333 556666666666
No 150
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=27.96 E-value=2.1e+02 Score=22.53 Aligned_cols=55 Identities=16% Similarity=0.236 Sum_probs=29.6
Q ss_pred HHHHHHhCCChHHHHHHHHHHHh---------cCCCCChHHHHHHHHHH--hhcCCCcHHHHHHHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQLR--KASMLDDSQVAEILNE 225 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYirY~L---------nEr~F~pd~VaDLi~Lr--kas~L~D~evaEiLnE 225 (278)
+++.+.+|-|.. -+|.|-+--| +-|-|+++.|+.|..++ +.+|++-+||.++|+.
T Consensus 4 ~eva~~~gvs~~-tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 4 GELAHLLGVPPS-TLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred HHHHHHHCcCHH-HHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 345555565543 3455555433 12346666666654433 2356677777766654
No 151
>PF11169 DUF2956: Protein of unknown function (DUF2956); InterPro: IPR021339 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=27.80 E-value=46 Score=27.97 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=16.3
Q ss_pred cCCCcCCCCCchhHHhhhhHhhh
Q 023705 96 IPGPRVGQSKLPWILAVPLAYVG 118 (278)
Q Consensus 96 IPGPRVg~s~lPwLlAlPLAylG 118 (278)
...+...++.|||+| |.|..+|
T Consensus 75 ~~~~~~~~~~LPW~L-L~lSW~g 96 (103)
T PF11169_consen 75 EISSQSRSSWLPWGL-LVLSWIG 96 (103)
T ss_pred cccccccccchhHHH-HHHHHHH
Confidence 345677889999986 5667777
No 152
>COG0283 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=27.67 E-value=76 Score=29.50 Aligned_cols=118 Identities=25% Similarity=0.310 Sum_probs=64.2
Q ss_pred cccccCCC-cCCCCCchhHHhhhhHhh----hhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCc
Q 023705 92 VTQAIPGP-RVGQSKLPWILAVPLAYV----GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNP 166 (278)
Q Consensus 92 vtQAIPGP-RVg~s~lPwLlAlPLAyl----G~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~ 166 (278)
.+=||=|| -.|-|.+-=++|--|.|. | ++||++--+- +.++-+--+.
T Consensus 5 ~~IAIDGPagsGKsTvak~lA~~Lg~~yldTG-----amYRa~a~~~-----------------------l~~~~~~~d~ 56 (222)
T COG0283 5 IIIAIDGPAGSGKSTVAKILAEKLGFHYLDTG-----AMYRAVALAA-----------------------LKHGVDLDDE 56 (222)
T ss_pred eEEEEeCCCccChHHHHHHHHHHhCCCeeccc-----HHHHHHHHHH-----------------------HHcCCCCccH
Confidence 34477788 677788877777666554 4 5566643221 3334444444
Q ss_pred hHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCC-CcHHHHHHHHHHHHhhhhhcCccccccc
Q 023705 167 PALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASML-DDSQVAEILNEISRRFVREKDEDALDEQ 242 (278)
Q Consensus 167 gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L-~D~evaEiLnE~srRiv~~~G~vmmn~~ 242 (278)
.++..|..+.-++...= .+..||.+.-++..-.+=+.- .||-. .-.+|-++|+++=|++.+..|.+|||=.
T Consensus 57 ~~~~~l~~~~~i~f~~~----~~v~l~gedvs~~ir~~~V~~-~aS~vA~~p~VR~~l~~~Qr~~a~~~~~~V~dGR 128 (222)
T COG0283 57 DALVALAKELDISFVND----DRVFLNGEDVSEEIRTEEVGN-AASKVAAIPEVREALVKLQRAFAKNGPGIVADGR 128 (222)
T ss_pred HHHHHHHHhCCceeccc----ceEEECCchhhhhhhhHHHHH-HHHHHHccHHHHHHHHHHHHHHHhcCCCEEEecC
Confidence 55555555554443211 223333333322211111111 11211 2467889999999999999888888865
No 153
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=27.29 E-value=72 Score=26.69 Aligned_cols=31 Identities=19% Similarity=0.443 Sum_probs=25.2
Q ss_pred HHHHhhcC---CCcHHHHHHHHHHHHhhhhhcCc
Q 023705 206 IQLRKASM---LDDSQVAEILNEISRRFVREKDE 236 (278)
Q Consensus 206 i~Lrkas~---L~D~evaEiLnE~srRiv~~~G~ 236 (278)
|+||..++ ++|.|+..++.||+.|+-+-+|.
T Consensus 33 iAlKAGLgeieI~d~eL~~aFeeiAaRFR~g~~~ 66 (98)
T PRK13848 33 IALKAGLGEIEIEEAELQAAFEELAKRFRGGKGA 66 (98)
T ss_pred HHHHcCccccccCHHHHHHHHHHHHHHHhcCCCc
Confidence 45665554 79999999999999999887764
No 154
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=27.13 E-value=3e+02 Score=22.01 Aligned_cols=9 Identities=44% Similarity=0.977 Sum_probs=4.6
Q ss_pred HhCCChHHH
Q 023705 175 KTGFSMEDV 183 (278)
Q Consensus 175 KTGFs~~EV 183 (278)
+.|||.+||
T Consensus 55 ~~G~sL~eI 63 (127)
T TIGR02044 55 QVGFSLEEC 63 (127)
T ss_pred HCCCCHHHH
Confidence 455555553
No 155
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.03 E-value=1.1e+02 Score=28.27 Aligned_cols=56 Identities=11% Similarity=0.242 Sum_probs=43.3
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHH
Q 023705 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNL 205 (278)
Q Consensus 145 KNamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDL 205 (278)
.+.++-+--..||..|++=-+..+|-.|....|.+.+|+-+ .|..+.+....-.|.
T Consensus 119 ~~~~~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~-----~L~s~~~~~avr~d~ 174 (225)
T COG2761 119 QDRFLEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFKA-----DLASDAAKDAVRQDE 174 (225)
T ss_pred HHHHHHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHHH-----HHhChHHHHHHHHHH
Confidence 46778888899999999999999999999999999988643 445555544443443
No 156
>PF10746 Phage_holin_6: Phage holin family 6; InterPro: IPR019682 This entry represents a protein conserved in Caudovirales (known as tailed bacteriophages). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis.
Probab=26.85 E-value=40 Score=26.34 Aligned_cols=46 Identities=26% Similarity=0.453 Sum_probs=34.8
Q ss_pred hhccccccccC---CC------cC--CCCCchhHHhhhhHhhhhhhhhhhhhhhhhc
Q 023705 87 EFTGSVTQAIP---GP------RV--GQSKLPWILAVPLAYVGVSFVIAFVKTVKKF 132 (278)
Q Consensus 87 eftG~vtQAIP---GP------RV--g~s~lPwLlAlPLAylG~TFviA~vRtvrK~ 132 (278)
.|+-.|.||.| ++ |. |-|---|.....++|.-+-...-++++++|+
T Consensus 4 df~n~vvkaaPi~~~a~A~~~a~~f~GLslneWfyiati~YtvlQig~~v~k~v~~~ 60 (66)
T PF10746_consen 4 DFNNEVVKAAPIVGTAGADVVARYFWGLSLNEWFYIATIAYTVLQIGYLVWKKVRDW 60 (66)
T ss_pred ccccchheecCCccchhHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777889998 33 33 6666679999999998777777788887765
No 157
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=26.82 E-value=2.9e+02 Score=21.69 Aligned_cols=52 Identities=10% Similarity=0.128 Sum_probs=28.5
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 023705 178 FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (278)
Q Consensus 178 Fs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRi 230 (278)
|+..||-+=..=..|++--|+.+.+.++++.-..-+ +.+++.++|++.-+.|
T Consensus 39 Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~-~~~~~~~~l~~~~~~l 90 (108)
T cd04773 39 YDPSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAG-GTEALAAALEQRRVAL 90 (108)
T ss_pred eCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCC-CHHHHHHHHHHHHHHH
Confidence 666666665554555666666666666666533222 2345555555544444
No 158
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.77 E-value=3.2e+02 Score=22.08 Aligned_cols=9 Identities=11% Similarity=0.420 Sum_probs=5.1
Q ss_pred HhCCChHHH
Q 023705 175 KTGFSMEDV 183 (278)
Q Consensus 175 KTGFs~~EV 183 (278)
+.||+.+||
T Consensus 55 ~lG~sL~eI 63 (127)
T TIGR02047 55 TLDMSLAEI 63 (127)
T ss_pred HcCCCHHHH
Confidence 556666554
No 159
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=26.63 E-value=78 Score=29.20 Aligned_cols=36 Identities=17% Similarity=0.409 Sum_probs=26.3
Q ss_pred cchhhHHhhHHHHHhcCCCC--------CCchH----HHHHHHHhCCC
Q 023705 144 NKNAMVCKTIDELFQKGGDA--------VNPPA----LKGLVQKTGFS 179 (278)
Q Consensus 144 NKNamLvkSLDeyFp~gRda--------l~~gv----Lk~L~~KTGFs 179 (278)
+++..|.++|.-||.+|.+- +|.+- |+++++-||.+
T Consensus 318 d~~~~L~~TL~~y~~~~~ni~~tA~~L~iHrNTL~YRL~kI~eltG~d 365 (385)
T PRK11477 318 DNNGLLRRTLAAWFRHNVQPLATSKALFIHRNTLEYRLNRISELTGLD 365 (385)
T ss_pred cCcchHHHHHHHHHHcCCCHHHHHHHhCCCHhhHHHHHHHHHHHhCcC
Confidence 34668999999999988763 33332 57888888887
No 160
>COG2704 DcuB Anaerobic C4-dicarboxylate transporter [General function prediction only]
Probab=26.47 E-value=47 Score=33.59 Aligned_cols=38 Identities=34% Similarity=0.556 Sum_probs=30.1
Q ss_pred hHHHHhcchhhHHhhhhhhhhccccccccCCCcCCCCCchhHHhhhhHhhhhhhhh
Q 023705 68 EVEVEEELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVI 123 (278)
Q Consensus 68 e~e~e~e~~wiqekaldlveftG~vtQAIPGPRVg~s~lPwLlAlPLAylG~TFvi 123 (278)
+-=+...++||++-+.|||+ .-||++|+.+++++ -++.
T Consensus 311 dTf~~~h~~~iK~~~~~lv~-----------------~~PW~~AvalF~vS-~lv~ 348 (436)
T COG2704 311 DTFVSAHIDEIKAVAGELVQ-----------------TYPWLLAVALFFVS-ALVN 348 (436)
T ss_pred HHHHHhhHHHHHHHHHHHHH-----------------cCcHHHHHHHHHHH-HHHh
Confidence 34466789999999999986 35999999999987 4443
No 161
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=26.13 E-value=33 Score=35.59 Aligned_cols=21 Identities=38% Similarity=0.329 Sum_probs=11.2
Q ss_pred hhhhHHHHhcchhhHHhhhhh
Q 023705 65 EEVEVEVEEELPWIQEKALDL 85 (278)
Q Consensus 65 ~e~e~e~e~e~~wiqekaldl 85 (278)
+|+|||+|||..|-+|--.-+
T Consensus 318 ~e~Eeeeee~~~f~~EV~~tv 338 (548)
T PF02459_consen 318 EEEEEEEEEEESFEEEVRRTV 338 (548)
T ss_pred CcccccccchhHHHHHHHHHH
Confidence 344555556566766643333
No 162
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.88 E-value=2.7e+02 Score=22.37 Aligned_cols=32 Identities=19% Similarity=0.192 Sum_probs=13.5
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 023705 178 FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLR 209 (278)
Q Consensus 178 Fs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lr 209 (278)
|+.++|-|=..=..|++--|+.+.+.+++++.
T Consensus 37 Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~ 68 (118)
T cd04776 37 YSRRDRARLKLILRGKRLGFSLEEIRELLDLY 68 (118)
T ss_pred cCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 44444444332223444444444444444443
No 163
>PF13565 HTH_32: Homeodomain-like domain
Probab=25.81 E-value=1.8e+02 Score=20.46 Aligned_cols=40 Identities=23% Similarity=0.325 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCC-CChHHHHHHHHHHhhcCC--CcHHHHHHH
Q 023705 184 LRKYIRYALNEKP-FNPDLVVNLIQLRKASML--DDSQVAEIL 223 (278)
Q Consensus 184 ~RKYirY~LnEr~-F~pd~VaDLi~Lrkas~L--~D~evaEiL 223 (278)
.++.|.-++.|.| +++..+++.|+-+-.-.+ +.+-|..+|
T Consensus 35 ~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 35 QRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 3466666767764 777777777776654433 665555443
No 164
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=25.79 E-value=1.5e+02 Score=23.24 Aligned_cols=26 Identities=31% Similarity=0.450 Sum_probs=23.4
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHH
Q 023705 161 GDAVNPPALKGLVQKTGFSMEDVLRK 186 (278)
Q Consensus 161 Rdal~~gvLk~L~~KTGFs~~EV~RK 186 (278)
.+.++...|+.+-.++|-+.+++|++
T Consensus 33 ~~~~t~~el~~~l~~~~~~~~~lin~ 58 (112)
T cd03034 33 KTPPTAAELRELLAKLGISPRDLLRT 58 (112)
T ss_pred cCCcCHHHHHHHHHHcCCCHHHHHhc
Confidence 46789999999999999999999987
No 165
>PF12335 SBF2: Myotubularin protein ; InterPro: IPR022096 This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with PF02141 from PFAM, PF03456 from PFAM, PF03455 from PFAM. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease.
Probab=25.76 E-value=53 Score=30.04 Aligned_cols=69 Identities=28% Similarity=0.430 Sum_probs=49.1
Q ss_pred chHHHHHHHHhCCC-hHHHHHHHHHH---HhcCCCCChHHHHHHH--HHHhhcCCCcHHHHHHHHHHHHhhhhhcCc
Q 023705 166 PPALKGLVQKTGFS-MEDVLRKYIRY---ALNEKPFNPDLVVNLI--QLRKASMLDDSQVAEILNEISRRFVREKDE 236 (278)
Q Consensus 166 ~gvLk~L~~KTGFs-~~EV~RKYirY---~LnEr~F~pd~VaDLi--~Lrkas~L~D~evaEiLnE~srRiv~~~G~ 236 (278)
+.+++.|+.+.|=. ..+.+.+|+.= .|++..|+ .|++|| +|...++.+|--+|.+|...+..+|++-++
T Consensus 47 ~av~~~lk~~~aR~~~~~~L~~~~~~~k~~L~~~qF~--~lv~lin~aLq~~s~~dd~~~Aa~LL~ls~~fyrkl~~ 121 (225)
T PF12335_consen 47 PAVLRALKSRSARQAFCRELSKHVKSNKAVLDDQQFD--YLVRLINCALQDCSESDDYGIAAALLPLSTAFYRKLSN 121 (225)
T ss_pred HHHHHHHccchHHHHHHHHHHHHHhcCCccCCHHHHH--HHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHcCc
Confidence 44555555554421 23455565532 36666775 788887 689999999999999999999999998654
No 166
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.73 E-value=4.1e+02 Score=26.88 Aligned_cols=59 Identities=15% Similarity=0.209 Sum_probs=47.0
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDLi 206 (278)
...+.+.|...+.+.+-.++..+++.|.+.+|-|+.+++. |.+-|. .+.-|.+.|.+++
T Consensus 177 ~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~--~~~It~e~V~~ll 238 (491)
T PRK14964 177 TDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYS--NNKISEKSVRDLL 238 (491)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHH
Confidence 4557778888888888899999999999999999987654 666664 3467888888765
No 167
>PF10389 CoatB: Bacteriophage coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 2IFO_A.
Probab=25.71 E-value=55 Score=23.91 Aligned_cols=24 Identities=29% Similarity=0.278 Sum_probs=21.4
Q ss_pred HHhhhhHhhhhhhhhhhhhhhhhc
Q 023705 109 ILAVPLAYVGVSFVIAFVKTVKKF 132 (278)
Q Consensus 109 LlAlPLAylG~TFviA~vRtvrK~ 132 (278)
++.+..+.||+...|+.||-+||.
T Consensus 22 i~~ig~avL~v~V~i~v~kwiRra 45 (46)
T PF10389_consen 22 IATIGGAVLGVIVGIAVYKWIRRA 45 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 678889999999999999999873
No 168
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=25.65 E-value=81 Score=21.03 Aligned_cols=28 Identities=29% Similarity=0.306 Sum_probs=23.0
Q ss_pred ChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023705 179 SMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 179 s~~EV~RKYirY~LnEr~F~pd~VaDLi 206 (278)
|++|+=+.||+.+|..-..|...+|.++
T Consensus 1 sl~~~E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 1 SLEEFEKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp -HHHHHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 5788999999999999999998888765
No 169
>PRK01905 DNA-binding protein Fis; Provisional
Probab=25.41 E-value=2e+02 Score=21.54 Aligned_cols=53 Identities=9% Similarity=0.159 Sum_probs=39.3
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
.+-+.|.+||-+-.+.=..+.++.. ++++=+.||+.+|.+-..|...+|+++.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~-------l~~~E~~~i~~aL~~~~gn~s~aAr~LG 61 (77)
T PRK01905 9 CIRDSLDQYFRDLDGSNPHDVYDMV-------LSCVEKPLLEVVMEQAGGNQSLAAEYLG 61 (77)
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHH-------HHHHHHHHHHHHHHHcCCCHHHHHHHHC
Confidence 4557888888886665556666553 4456689999999999999888876543
No 170
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.40 E-value=96 Score=27.97 Aligned_cols=40 Identities=28% Similarity=0.419 Sum_probs=31.6
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccc
Q 023705 202 VVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQ 242 (278)
Q Consensus 202 VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~ 242 (278)
..||-..=-|.-|+|+||.|...|| .+++++=+++|+|+.
T Consensus 96 l~dL~dii~~~f~sdeev~ey~~ei-~~l~e~g~ts~~~vt 135 (170)
T COG4860 96 LSDLADIIYAAFLSDEEVKEYEDEI-KALMEEGNTSFLDVT 135 (170)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH-HHHHHcCCceEeehh
Confidence 3444444456779999999999998 567889999999887
No 171
>PRK00056 mtgA monofunctional biosynthetic peptidoglycan transglycosylase; Provisional
Probab=25.31 E-value=4.7e+02 Score=24.22 Aligned_cols=57 Identities=9% Similarity=0.081 Sum_probs=38.5
Q ss_pred cCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccchhhhhhcccCCc
Q 023705 193 NEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQPPMQALFVFDPV 254 (278)
Q Consensus 193 nEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~~avqalf~~~~~ 254 (278)
+||.+.--..+=+++++=-..+|.+||=|+-..+. .+|+=+--.+.|.|..|||+|-
T Consensus 127 ~~rs~~RK~~E~~lA~~lE~~~sK~~ILe~YLN~v-----~~G~g~yGi~aAa~~YFgk~~~ 183 (236)
T PRK00056 127 PGRSWVRKGLEAPLTLMIELVWSKRRILEVYLNIA-----EWGPGIFGAEAAARHYFGKPAS 183 (236)
T ss_pred CCCcHhHHHHHHHHHHHHHHhCCHHHHHHHHHHHh-----hcCCCchHHHHHHHHHcCCChh
Confidence 35555555566666666667777777777633322 4677566667999999999874
No 172
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=25.21 E-value=64 Score=22.82 Aligned_cols=59 Identities=14% Similarity=0.133 Sum_probs=37.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhh-cCCCcHHHHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKA-SMLDDSQVAEILNEIS 227 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrka-s~L~D~evaEiLnE~s 227 (278)
++-++...|......-++.|...+++-.|++|.|-.+|..=.. -..+-+=+..||+.-.
T Consensus 2 ~~~~e~~~~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~~~Yi~~Il~~W~ 61 (77)
T PF07261_consen 2 FEFYEKNFGRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRSFNYIEKILNNWK 61 (77)
T ss_dssp HHHHHCCCTSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--SHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 4455666788888888999999999889999999776654332 1234444555555543
No 173
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.19 E-value=1.2e+02 Score=20.93 Aligned_cols=32 Identities=28% Similarity=0.302 Sum_probs=25.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 023705 177 GFSMEDVLRKYIRYALNEKPFNPDLVVNLIQL 208 (278)
Q Consensus 177 GFs~~EV~RKYirY~LnEr~F~pd~VaDLi~L 208 (278)
-|+..||.+=-.-..|++.-|+++.++.+++|
T Consensus 38 ~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~l 69 (70)
T smart00422 38 LYSDEDLERLRFIKRLKELGFSLEEIKELLEL 69 (70)
T ss_pred ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 38888887666666678899999999998876
No 174
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.14 E-value=4.4e+02 Score=27.66 Aligned_cols=58 Identities=19% Similarity=0.292 Sum_probs=41.7
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi 206 (278)
..+.+.|.+.+.+.+-.++..+++.|.+.++-++.++ +.+.+ .+.++.-+.+.|.+++
T Consensus 181 ~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~lLeqll--~~g~~~It~d~V~~~l 241 (624)
T PRK14959 181 AGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLLGQVL--ALGESRLTIDGARGVL 241 (624)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHH--HhcCCCcCHHHHHHHh
Confidence 3456677777777777799999999999999987754 44544 3466677777776543
No 175
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=25.01 E-value=57 Score=26.01 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=15.7
Q ss_pred HHHHhhc--CCCcHHHHHHHHHH
Q 023705 206 IQLRKAS--MLDDSQVAEILNEI 226 (278)
Q Consensus 206 i~Lrkas--~L~D~evaEiLnE~ 226 (278)
.|+|.|. |.|++|+.|+|.-.
T Consensus 75 ~H~~~Al~~GaT~eEI~e~i~~~ 97 (124)
T COG0599 75 VHVRAALENGATKEEIAEAIAVA 97 (124)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHH
Confidence 4566665 99999999988643
No 176
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=24.98 E-value=64 Score=25.52 Aligned_cols=41 Identities=17% Similarity=0.298 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 023705 180 MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (278)
Q Consensus 180 ~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE 225 (278)
..|.||+|+.+...+=||+ +--.|=+-+|||+.||.+|-.+
T Consensus 2 ~~~~l~~~f~~i~~~V~~~-----~Wk~laR~LGLse~~I~~i~~~ 42 (96)
T cd08315 2 PQETLRRSFDHFIKEVPFD-----SWNRLMRQLGLSENEIDVAKAN 42 (96)
T ss_pred cHhHHHHHHHHHHHHCCHH-----HHHHHHHHcCCCHHHHHHHHHH
Confidence 4688999999988887753 4445556789999999888654
No 177
>PRK11677 hypothetical protein; Provisional
Probab=24.94 E-value=59 Score=27.78 Aligned_cols=22 Identities=18% Similarity=0.298 Sum_probs=15.8
Q ss_pred chhHHhhhhHhhhhhhhhhhhh
Q 023705 106 LPWILAVPLAYVGVSFVIAFVK 127 (278)
Q Consensus 106 lPwLlAlPLAylG~TFviA~vR 127 (278)
|+|+.++-.+.+|+.+.+.+.|
T Consensus 1 M~W~~a~i~livG~iiG~~~~R 22 (134)
T PRK11677 1 MTWEYALIGLVVGIIIGAVAMR 22 (134)
T ss_pred CcHHHHHHHHHHHHHHHHHHHh
Confidence 5799999888888555554444
No 178
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=24.82 E-value=49 Score=26.57 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=28.6
Q ss_pred hHHHHHhcCCCCCCchHHHHHHHHhCCChHHHH
Q 023705 152 TIDELFQKGGDAVNPPALKGLVQKTGFSMEDVL 184 (278)
Q Consensus 152 SLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~ 184 (278)
.|..||+.=++.+.....|.+.++.|+|-.+|=
T Consensus 6 dl~~~l~~Ia~~~~~~~wK~faR~lglse~~Id 38 (97)
T cd08316 6 DLSKHIPDIADVMTLKDVKKFVRKSGLSEPKID 38 (97)
T ss_pred cHHHhhHHHHHHcCHHHHHHHHHHcCCCHHHHH
Confidence 367899998999999999999999999987764
No 179
>PRK13749 transcriptional regulator MerD; Provisional
Probab=24.71 E-value=1.1e+02 Score=25.35 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=39.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh---------cCCCCChHHHHHHHHHH--hhcCCCcHHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQLR--KASMLDDSQVAEILNE 225 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~L---------nEr~F~pd~VaDLi~Lr--kas~L~D~evaEiLnE 225 (278)
..++.++||-|..- +|=|=+=-| +=|-|+++.|+.|-.++ +.+|++=+||+++|.-
T Consensus 6 IgelA~~~gvS~~t-iR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 6 VSRLALDAGVSVHI-VRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred HHHHHHHHCCCHHH-HHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 45677888877543 355532222 33568899999888888 5899999999888864
No 180
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=24.66 E-value=2.7e+02 Score=22.08 Aligned_cols=52 Identities=8% Similarity=0.045 Sum_probs=38.0
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi 206 (278)
.+-..|++||..--+.-..+.++.. ++++=|.||+.+|..-..|....|.++
T Consensus 27 ~~~~~l~~~~~~l~~~~~~~~~~~~-------l~~~Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 27 SVKQALKNYFAQLNGQDVNDLYELV-------LAEVEAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHHhcCCCchhHHHHH-------HHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 3556789999875554455666654 346678999999999999988887654
No 181
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=24.65 E-value=69 Score=23.14 Aligned_cols=27 Identities=15% Similarity=0.273 Sum_probs=20.0
Q ss_pred Cccccccc----hhhhhhcccCCccchhhhhhh
Q 023705 235 DEDALDEQ----PPMQALFVFDPVHNICCFLHM 263 (278)
Q Consensus 235 G~vmmn~~----~avqalf~~~~~~~~~~~~~~ 263 (278)
..+|+|-+ .|++..|.. .+...|..|.
T Consensus 58 ~~ii~D~~~~~~~Ai~~vfP~--~~~~~C~~H~ 88 (93)
T PF10551_consen 58 KVIISDFDKALINAIKEVFPD--ARHQLCLFHI 88 (93)
T ss_pred eeeeccccHHHHHHHHHHCCC--ceEehhHHHH
Confidence 36788887 788999955 5566677775
No 182
>cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-
Probab=24.64 E-value=4.9e+02 Score=22.98 Aligned_cols=138 Identities=14% Similarity=0.161 Sum_probs=67.9
Q ss_pred hcchhhHHhhhhhhhhccccccccCCCcCCCCCchhHHhhhhHhh--hhhhhhhhhhhhhhcC-Chhhhhhhhhcchh--
Q 023705 73 EELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYV--GVSFVIAFVKTVKKFN-SPKFKRKKLVNKNA-- 147 (278)
Q Consensus 73 ~e~~wiqekaldlveftG~vtQAIPGPRVg~s~lPwLlAlPLAyl--G~TFviA~vRtvrK~~-SPraKRkR~VNKNa-- 147 (278)
.+.|=|++|+..+........+. ++-.+..++...++ |+-|.-+|+=+ ..+. ..+.+..-.+++.+
T Consensus 118 ~~~~~l~~k~~~~~~~~~~~~~~--------~~~~~~~~lv~~~~lEgi~f~s~F~~~-~~l~~~g~m~g~~~~i~~I~R 188 (288)
T cd01049 118 ETDPALKKKADWILRWYDNLDDN--------TKESFAERLVAFAILEGIFFYSGFAAI-FWLARRGKMPGLAEIIELISR 188 (288)
T ss_pred hcCHHHHHHHHHHHHHHHhhhhc--------hHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCccchHHHhHHHHc
Confidence 56688999998888777765432 44556666654322 64443333322 2221 11222222222211
Q ss_pred -------hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHH
Q 023705 148 -------MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVA 220 (278)
Q Consensus 148 -------mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~eva 220 (278)
+-+.-+..++.++.+ +.....++.....-=...++-.+|++|++.+. ..|++.+++.
T Consensus 189 DE~~H~~~~~~~~~~l~~~~~~-~~~~~~~~~v~~l~~~av~~E~~~~~~~~~~~---------------~~g~~~~~~~ 252 (288)
T cd01049 189 DESLHGDFACLLIRELLNENPE-LFTEEFKEEVYELIKEAVELEKEFARDLLPDG---------------ILGLNKEDMK 252 (288)
T ss_pred cHHHHHHHHHHHHHHHHHhCcc-ccchhHHHHHHHHHHHHHHHHHHHHHHhcCCC---------------CCCcCHHHHH
Confidence 122223333322221 11111111111111124445555666655443 6789999999
Q ss_pred HHHHHHHHhhhhhcC
Q 023705 221 EILNEISRRFVREKD 235 (278)
Q Consensus 221 EiLnE~srRiv~~~G 235 (278)
.-+.-++.|....-|
T Consensus 253 ~yi~y~an~~l~~lG 267 (288)
T cd01049 253 QYIEYVANRRLENLG 267 (288)
T ss_pred HHHHHHHHHHHHHCC
Confidence 999989888877655
No 183
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=24.38 E-value=1.1e+02 Score=23.87 Aligned_cols=37 Identities=22% Similarity=0.362 Sum_probs=16.4
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 185 RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
+.|++..++-+...|-.+..=+.-| |++++.|.++|.
T Consensus 31 ~~~v~~~~~~~~~G~~~I~~~L~~k---Gi~~~~i~~~l~ 67 (121)
T PF02631_consen 31 ESYVRSRLRRKGKGPRRIRQKLKQK---GIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHT---T--HHHHHHHHT
T ss_pred HHHHHHhcccccccHHHHHHHHHHH---CCChHHHHHHHH
Confidence 4455555555555555544332222 555555555555
No 184
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=24.35 E-value=5e+02 Score=23.01 Aligned_cols=59 Identities=17% Similarity=0.275 Sum_probs=43.3
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDLi 206 (278)
...+.+-|.+++.+.+-.++..+++.|...+|-+...+.. |-+.|. .+..+.+.|.+++
T Consensus 178 ~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~--~~~it~~~v~~~~ 239 (355)
T TIGR02397 178 LEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFG--NGNITYEDVNELL 239 (355)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhc--CCCCCHHHHHHHh
Confidence 3456777888888877789999999999999998876543 444453 3557888776544
No 185
>KOG4129 consensus Exopolyphosphatases and related proteins [Energy production and conversion]
Probab=24.28 E-value=1e+02 Score=30.77 Aligned_cols=95 Identities=24% Similarity=0.352 Sum_probs=62.8
Q ss_pred hhHHhhhh----hhhhcccccccc--------CCCcCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhc
Q 023705 77 WIQEKALD----LVEFTGSVTQAI--------PGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVN 144 (278)
Q Consensus 77 wiqekald----lveftG~vtQAI--------PGPRVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VN 144 (278)
-+..|-++ .||+.||-++-| |+-+--+. +++--..| |++|-+.-+=++=+||
T Consensus 134 p~e~~~~~a~~~~Ie~~gScsTLV~~y~l~~~~~~~~~~~------n~A~LL~g-~ILiDt~nm~~ek~s~--------- 197 (377)
T KOG4129|consen 134 PDEDKHLPACPRIIELSGSCSTLVSRYILEELQELNTRQA------NLARLLLG-PILIDTGNMRKEKTSP--------- 197 (377)
T ss_pred cccccCCCccceeEEeecchHHHHHHHHHhhcchhhhHHH------HHHHHhhc-ceEEeccccccccCCh---------
Confidence 45555555 588888866443 55433111 34444557 8888877663333444
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHH----hCCChHHHHHHHH
Q 023705 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQK----TGFSMEDVLRKYI 188 (278)
Q Consensus 145 KNamLvkSLDeyFp~gRdal~~gvLk~L~~K----TGFs~~EV~RKYi 188 (278)
|-..+++-|.++||.++. .-...++.|+.+ .|||-++|+||=+
T Consensus 198 kd~~~v~kLe~~~p~~l~-~r~~~fd~Lk~ak~d~sgls~~~iLrKD~ 244 (377)
T KOG4129|consen 198 KDVEIVKKLEELFPVKLP-ERSEFFDELKSAKFDISGLSTDDILRKDL 244 (377)
T ss_pred hHHHHHHHHHHHcCCCch-hHHHHHHHHHHhhcccccCcHHHHHHHHH
Confidence 445589999999997655 455677777765 6999999999965
No 186
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.13 E-value=64 Score=22.33 Aligned_cols=55 Identities=25% Similarity=0.367 Sum_probs=35.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh--------cCCCCChHHHHHH---HHHHhhcCCCcHHHHHHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYAL--------NEKPFNPDLVVNL---IQLRKASMLDDSQVAEILNE 225 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~L--------nEr~F~pd~VaDL---i~Lrkas~L~D~evaEiLnE 225 (278)
++++++.+|-+. +.+|.|.+=-| +-+-|+++.|.-| ..|++ .|++-+||+++|++
T Consensus 3 i~eva~~~gvs~-~tlr~y~~~gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 3 IKEVAKLLGVSP-STLRYYEREGLLPPPRDENGYRYYSEEDVERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHTTTTH-HHHHHHHHTTSSTTBESTTSSEEE-HHHHHHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHHCcCH-HHHHHHHHhcCcccccccCceeeccHHHHHHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 456778888764 45677765322 1256777777655 45666 99999999999875
No 187
>PRK09358 adenosine deaminase; Provisional
Probab=23.90 E-value=4.9e+02 Score=23.55 Aligned_cols=23 Identities=22% Similarity=-0.018 Sum_probs=16.8
Q ss_pred CCCcHHHHHHHHHHHHhhhhhcC
Q 023705 213 MLDDSQVAEILNEISRRFVREKD 235 (278)
Q Consensus 213 ~L~D~evaEiLnE~srRiv~~~G 235 (278)
||+-+++-+++.+..++..+++|
T Consensus 111 gl~~~~~~~a~~~~~~~a~~~~g 133 (340)
T PRK09358 111 GLPLEEVVEAVLDGLRAAEAEFG 133 (340)
T ss_pred CCCHHHHHHHHHHHHHHHHHhcC
Confidence 66666777777777777788887
No 188
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=23.86 E-value=2.9e+02 Score=27.97 Aligned_cols=46 Identities=15% Similarity=0.341 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH------HhhhhhcCccccc
Q 023705 195 KPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS------RRFVREKDEDALD 240 (278)
Q Consensus 195 r~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s------rRiv~~~G~vmmn 240 (278)
-+++|+.+++||.|=..-.+|...+.++|.+.. ..|++++|-..++
T Consensus 367 ~~l~p~~l~~Li~lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii~~~gl~~is 418 (478)
T TIGR00133 367 CGLKPSDLAELIKLIKEGKISGKSAKQLIEEMLENGGDPSKLIEELGLEQIS 418 (478)
T ss_pred cCCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcCCCHHHHHHhcCCcccC
Confidence 379999999999999999999999999999884 6688999876553
No 189
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=23.67 E-value=77 Score=24.12 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=18.1
Q ss_pred CCCcHHHHHHHHHHHHhhhhhcCc
Q 023705 213 MLDDSQVAEILNEISRRFVREKDE 236 (278)
Q Consensus 213 ~L~D~evaEiLnE~srRiv~~~G~ 236 (278)
.|+|+||.++.+.+-..+-+++|-
T Consensus 68 TLt~~ev~~~~~~i~~~l~~~~~~ 91 (94)
T PF03147_consen 68 TLTDEEVNEIHDKIIKALEKKLGA 91 (94)
T ss_dssp ---HHHHHHHHHHHHHHHHHTCT-
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCc
Confidence 589999999999999888888874
No 190
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=23.63 E-value=1.5e+02 Score=23.75 Aligned_cols=37 Identities=24% Similarity=0.461 Sum_probs=26.3
Q ss_pred HHhhH-HHHHhcCCCCCCchHHHHHHHHhCCChHHHHH
Q 023705 149 VCKTI-DELFQKGGDAVNPPALKGLVQKTGFSMEDVLR 185 (278)
Q Consensus 149 LvkSL-DeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R 185 (278)
+.+.| ..+|..+++--+..+|+++..+.|++.+++..
T Consensus 107 ~~~~l~~a~~~~~~~i~~~~~l~~ia~~~Gld~~~~~~ 144 (193)
T cd03025 107 MLKAIQRAHYVEGRDLADTEVLRELAIELGLDVEEFLE 144 (193)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence 34443 44666677777777999999999998876543
No 191
>PF13934 ELYS: Nuclear pore complex assembly
Probab=23.44 E-value=4.2e+02 Score=23.54 Aligned_cols=103 Identities=14% Similarity=0.120 Sum_probs=64.3
Q ss_pred cccCCCcCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHH
Q 023705 94 QAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLV 173 (278)
Q Consensus 94 QAIPGPRVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~gvLk~L~ 173 (278)
.-++.|++.+.--+||+..=+..-.-...++++|+++-.-+....-.- =..+.-+.++-| .+.
T Consensus 99 ~~L~~ps~~~~~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s~~~~~~--~~~~La~~~v~E---------------Af~ 161 (226)
T PF13934_consen 99 ELLSHPSLIPWFPDKILQALLRRGDPKLALRYLRAVGPPLSSPEALTL--YFVALANGLVTE---------------AFS 161 (226)
T ss_pred HHhCCCCCCcccHHHHHHHHHHCCChhHHHHHHHhcCCCCCCHHHHHH--HHHHHHcCCHHH---------------HHH
Confidence 334889887666679999888887888999999998776554411110 011111222333 233
Q ss_pred HHhCCCh---HHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHH
Q 023705 174 QKTGFSM---EDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQ 218 (278)
Q Consensus 174 ~KTGFs~---~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~e 218 (278)
-...|.. .+.+.+-+.+.+++.+ ..+.+.+|+.| -|+++|
T Consensus 162 ~~R~~~~~~~~~l~e~l~~~~~~~~~-~~~~~~~Ll~L----Pl~~~E 204 (226)
T PF13934_consen 162 FQRSYPDELRRRLFEQLLEHCLEECA-RSGRLDELLSL----PLDEEE 204 (226)
T ss_pred HHHhCchhhhHHHHHHHHHHHHHHhh-hhhHHHHHHhC----CCChHH
Confidence 2233333 4588999999998887 56777777764 455555
No 192
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=23.43 E-value=1.2e+02 Score=27.66 Aligned_cols=121 Identities=15% Similarity=0.127 Sum_probs=0.0
Q ss_pred cCCCcCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCch--------
Q 023705 96 IPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPP-------- 167 (278)
Q Consensus 96 IPGPRVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal~~g-------- 167 (278)
||+--. ++-+.+-|+. .++-+.|.+ -..-..++++....+..+-+.|.+.+..-......+
T Consensus 69 iPf~~~-------llp~~~~~fP-~lLPstF~~---~~q~~~~~~~~~~~r~~~~~~Lq~~l~~~~~~~~~~~~~~~~~~ 137 (268)
T PF07766_consen 69 IPFAEY-------LLPLLVKYFP-NLLPSTFWS---PSQREEFLKKRLKARKELAKFLQETLEEISKSSKNSNKQERKKL 137 (268)
T ss_dssp ----------------------------------------------HHHHHHHHHHHHHHHHTT-----GGG-SSHHHHH
T ss_pred hhHHHH-------HHHHHHHHhh-hcChHHHcc---cchHHHHHHHHHHHhHhhHHHHHHHHHHhccccccchhhhHHHH
Q ss_pred --HHHHHHHHhCCChHHHH----------------------------------HHHHHHHhcCCCCChHHHHHHHHHHhh
Q 023705 168 --ALKGLVQKTGFSMEDVL----------------------------------RKYIRYALNEKPFNPDLVVNLIQLRKA 211 (278)
Q Consensus 168 --vLk~L~~KTGFs~~EV~----------------------------------RKYirY~LnEr~F~pd~VaDLi~Lrka 211 (278)
.++++....--+.+||+ +-++||-|+.+-----.-+.+|.--..
T Consensus 138 ~~~~~kv~~~~~~s~~eil~~~~lF~d~~~Ld~Lsr~~L~~L~r~~~l~~~~~~~~lr~rL~~~~~~l~~dD~~i~~eGv 217 (268)
T PF07766_consen 138 SEFFKKVRSGGHPSNEEILKVAKLFKDELTLDNLSRPHLRALCRLLGLTPFGPSSLLRRRLRKRLRYLKQDDRLIKREGV 217 (268)
T ss_dssp HHHHHHHHT-BTB-HHHHHHHHTTS-HHHHHHHS-HHHHHHHHHHTT----SSHHHHHHHHHHHHHHHHHHHHHHHHH-G
T ss_pred HHHHHHhccCCCCCHHHHHHHHHhcCCCcccccCCHHHHHHHHHHhccCcCCchHHHHHHHHHHHHHHHHHHHHHHHhcc
Q ss_pred cCCCcHHHHHHHHHHH
Q 023705 212 SMLDDSQVAEILNEIS 227 (278)
Q Consensus 212 s~L~D~evaEiLnE~s 227 (278)
..||++|+.++..+++
T Consensus 218 ~~Ls~~EL~~Ac~~RG 233 (268)
T PF07766_consen 218 DSLSEEELQDACYERG 233 (268)
T ss_dssp GGS-HHHHHHHHHHTT
T ss_pred ccCCHHHHHHHHHHhC
No 193
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.41 E-value=1.6e+02 Score=20.05 Aligned_cols=33 Identities=24% Similarity=0.244 Sum_probs=17.1
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHH
Q 023705 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (278)
Q Consensus 185 RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~ev 219 (278)
+.||.--.+.+. +|. +..|.+|-.++|++-+++
T Consensus 26 ~~~i~~~e~g~~-~~~-~~~l~~i~~~~~v~~~~l 58 (64)
T PF12844_consen 26 RSTISKIENGKR-KPS-VSTLKKIAEALGVSLDEL 58 (64)
T ss_dssp HHHHHHHHTTSS---B-HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCCCc-CCC-HHHHHHHHHHhCCCHHHH
Confidence 455555555443 333 445566777777776554
No 194
>PF09677 TrbI_Ftype: Type-F conjugative transfer system protein (TrbI_Ftype); InterPro: IPR014115 This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [, ].
Probab=23.30 E-value=1.8e+02 Score=23.97 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=34.7
Q ss_pred HHhhHHHHHhc-CCCCCCchHHHHHHHHhCCChHHHHHHHHH
Q 023705 149 VCKTIDELFQK-GGDAVNPPALKGLVQKTGFSMEDVLRKYIR 189 (278)
Q Consensus 149 LvkSLDeyFp~-gRdal~~gvLk~L~~KTGFs~~EV~RKYir 189 (278)
+=+.+|+|.+. .+.++++..-+.+-+.+.-.+++.+..|=+
T Consensus 38 l~~tv~~f~~~~a~~~lt~~q~~a~t~~F~~aL~~~L~~~~~ 79 (111)
T PF09677_consen 38 LKGTVDEFVQQLARSSLTPEQVEALTQRFMQALEASLAEYQA 79 (111)
T ss_pred HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44678999887 889999999999999988888888888754
No 195
>PRK14530 adenylate kinase; Provisional
Probab=23.30 E-value=1.3e+02 Score=25.47 Aligned_cols=57 Identities=19% Similarity=0.275 Sum_probs=32.7
Q ss_pred HHHHHHHHhCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023705 168 ALKGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 168 vLk~L~~KTGF---s~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~ 226 (278)
.-+.|.++.|| ++.|++|+++....++..-.-+...+. ++.+....|+.+.++|.+.
T Consensus 19 ~~~~La~~~~~~~i~~g~~lr~~~~~~~~~~~~~~~~~~~~--~~~g~~~~d~~~~~~l~~~ 78 (215)
T PRK14530 19 QSSNLAEEFGVEHVTTGDALRANKQMDISDMDTEYDTPGEY--MDAGELVPDAVVNEIVEEA 78 (215)
T ss_pred HHHHHHHHhCCeEEeccHHHHHhccCCcccccchHHHHHHH--HHcCCCCCHHHHHHHHHHH
Confidence 45788899999 899999988743333322112223332 3444445665555555544
No 196
>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Probab=23.15 E-value=1.8e+02 Score=23.69 Aligned_cols=47 Identities=19% Similarity=0.202 Sum_probs=33.9
Q ss_pred CCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCc
Q 023705 160 GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDD 216 (278)
Q Consensus 160 gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D 216 (278)
++.-.-...+++|.+++|..... -.-++.|+.+.|.+.+=+++|++|
T Consensus 96 g~~~~~~~~~~~lr~~~g~~~~p----------~~~~~~p~~~~~~~~il~~~~~~~ 142 (144)
T TIGR03290 96 GHAVPINDEIKELRKELGLDEIP----------PTTHKYPEALEEVQKLIKALEFDE 142 (144)
T ss_pred CCCCCccHHHHHHHHHcCCCCCC----------CccccCHHHHHHHHHHHHHhChhh
Confidence 33334446678999999973111 233889999999999999999876
No 197
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=22.99 E-value=1.1e+02 Score=21.47 Aligned_cols=47 Identities=17% Similarity=0.220 Sum_probs=35.4
Q ss_pred HhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023705 175 KTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (278)
Q Consensus 175 KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srR 229 (278)
..|++..| .+-+.|+|...+.|.+.+++ .+|++-+.|-.+|+...++
T Consensus 3 ~~gLs~~E--~~vy~~Ll~~~~~t~~eIa~------~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 3 VLGLSENE--AKVYLALLKNGPATAEEIAE------ELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHCHHHHH--HHHHHHHHHHCHEEHHHHHH------HHTSSHHHHHHHHHHHHHT
T ss_pred cCCcCHHH--HHHHHHHHHcCCCCHHHHHH------HHCcCHHHHHHHHHHHHHC
Confidence 44555444 57778888888888877665 6789999999999987653
No 198
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=22.97 E-value=1.7e+02 Score=23.36 Aligned_cols=36 Identities=17% Similarity=0.423 Sum_probs=26.4
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV 183 (278)
++-.-.+.||..+++--+..+|..+..+.|++.+++
T Consensus 105 ~~~~lf~a~~~~~~~i~~~~~l~~~a~~~Gld~~~~ 140 (192)
T cd03022 105 FARAVFRALWGEGLDIADPAVLAAVAAAAGLDADEL 140 (192)
T ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHcCCCHHHH
Confidence 333334556777887677789999999999987654
No 199
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.89 E-value=2.3e+02 Score=21.98 Aligned_cols=34 Identities=21% Similarity=0.187 Sum_probs=15.2
Q ss_pred CChHHHHH-HHHHHHhcCCCCChHHHHHHHHHHhh
Q 023705 178 FSMEDVLR-KYIRYALNEKPFNPDLVVNLIQLRKA 211 (278)
Q Consensus 178 Fs~~EV~R-KYirY~LnEr~F~pd~VaDLi~Lrka 211 (278)
|+..||.| +.|..+.+|--|+.+.+..++++...
T Consensus 38 Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~ 72 (96)
T cd04774 38 YSEEDLKRLERILRLREVLGFSLQEVTHFLERPLE 72 (96)
T ss_pred ECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccc
Confidence 34444444 22333333355555555555554443
No 200
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=22.84 E-value=2.1e+02 Score=22.82 Aligned_cols=79 Identities=18% Similarity=0.301 Sum_probs=48.6
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s 227 (278)
+.-.-.+.||..+++--+..+|..+..+.|++.+++... ++|.++.+.+.+.-
T Consensus 105 ~~~al~~a~~~~~~~i~~~~vl~~~~~~~Gld~~~~~~~---------------------------~~~~~~~~~~~~~~ 157 (193)
T PF01323_consen 105 FADALFRAYFVEGRDISDPDVLAEIAEEAGLDPDEFDAA---------------------------LDSPEVKAALEEDT 157 (193)
T ss_dssp HHHHHHHHHHTSST-TSSHHHHHHHHHHTT--HHHHHHH---------------------------HTSHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHHHcCCcHHHHHHH---------------------------hcchHHHHHHHHHH
Confidence 333444667888899888889999999999988875432 24456666665544
Q ss_pred HhhhhhcC-----ccccccchhhhhhcccCCccch
Q 023705 228 RRFVREKD-----EDALDEQPPMQALFVFDPVHNI 257 (278)
Q Consensus 228 rRiv~~~G-----~vmmn~~~avqalf~~~~~~~~ 257 (278)
++. .++| ++++|=. +.+||-|+.+.+
T Consensus 158 ~~a-~~~gv~GvP~~vv~g~---~~~~G~~~~~~l 188 (193)
T PF01323_consen 158 AEA-RQLGVFGVPTFVVNGK---YRFFGADRLDEL 188 (193)
T ss_dssp HHH-HHTTCSSSSEEEETTT---EEEESCSSHHHH
T ss_pred HHH-HHcCCcccCEEEECCE---EEEECCCCHHHH
Confidence 443 3444 3444433 577888776654
No 201
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=22.80 E-value=83 Score=23.92 Aligned_cols=38 Identities=29% Similarity=0.577 Sum_probs=16.3
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 182 DVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 182 EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
+|+|| |||||+ ++.+.+.++.+|= ..-+|.+|+...|+
T Consensus 3 dILrk-LRyal~---l~d~~m~~if~l~-~~~vs~~el~a~lr 40 (68)
T PF07308_consen 3 DILRK-LRYALD---LKDDDMIEIFALA-GFEVSKAELSAWLR 40 (68)
T ss_pred HHHHH-HHHHHc---CChHHHHHHHHHc-CCccCHHHHHHHHC
Confidence 44554 455554 3334444444432 23344444444443
No 202
>PRK13481 glycosyltransferase; Provisional
Probab=22.79 E-value=1.6e+02 Score=27.34 Aligned_cols=55 Identities=15% Similarity=0.199 Sum_probs=36.4
Q ss_pred cCCCCChHHHHHHHHHHhhcCCCcHHHHHH-HHHHHHhhhhhcCccccccchhhhhhcccCC
Q 023705 193 NEKPFNPDLVVNLIQLRKASMLDDSQVAEI-LNEISRRFVREKDEDALDEQPPMQALFVFDP 253 (278)
Q Consensus 193 nEr~F~pd~VaDLi~Lrkas~L~D~evaEi-LnE~srRiv~~~G~vmmn~~~avqalf~~~~ 253 (278)
+||-+.--.-+=.++++=-.-+|.+||=|. ||.+ .+|.=.--.+.|.|..|||+|
T Consensus 111 ~~rt~~RK~~E~~~A~~lE~~~SK~eILe~YLN~v------~~G~g~yGi~aAA~~YFgK~~ 166 (232)
T PRK13481 111 NERSFTRKVKELFVAHRVEKQYSKNEILSFYLNNI------YFGDNQYTLEGAANHYFGTTV 166 (232)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHc------ccCCchHHHHHHHHHHcCCCc
Confidence 456666666666666666667777776665 3322 355544456699999999998
No 203
>KOG1869 consensus Splicing coactivator SRm160/300, subunit SRm300 [RNA processing and modification]
Probab=22.68 E-value=1.2e+02 Score=30.79 Aligned_cols=52 Identities=23% Similarity=0.095 Sum_probs=38.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCCCCh---------------------HHHHHHHHHHhhcCCCcHHHH
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNP---------------------DLVVNLIQLRKASMLDDSQVA 220 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~LnEr~F~p---------------------d~VaDLi~Lrkas~L~D~eva 220 (278)
|+.+...-|++-.||.+|---|-+|+-.=++ -.+..+.|+|.|+||.|.+|.
T Consensus 73 ~ee~lleqg~seeei~~k~~e~rknl~~~a~~~nE~~~~qe~S~teThqlara~eeq~e~~raAlgL~e~qv~ 145 (425)
T KOG1869|consen 73 LEESLLEQGLSEEEILSKVQEDRKNLLLRAKLTNEEQEDQEMSSTETHQLARATEEQHEHERAALGLKELQVQ 145 (425)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhHHhhccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHhCcchhhcc
Confidence 4556667799999999998777655432222 246678999999999999875
No 204
>cd08801 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.65 E-value=2.3e+02 Score=23.83 Aligned_cols=67 Identities=27% Similarity=0.349 Sum_probs=44.4
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 023705 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISR 228 (278)
Q Consensus 149 LvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~sr 228 (278)
||.+||.=-.+|.| -|.|.+|-+.+. ||-|.-+- +=--+.+-||-.-|--.+=+=.+++-+|.|++|
T Consensus 9 lC~~LD~p~~kg~D------WR~LA~kL~iDR------yl~yFatk-~SPT~viLdLWEa~~~~~g~L~~La~aleeiGr 75 (98)
T cd08801 9 ICATFDTPNAKGKD------WQMLAQKNSIDR------NLSYFATQ-SSPSAVILSLWEARHQHDGDLDSLACALEEIGR 75 (98)
T ss_pred HHHHcCCCCCCCcc------HHHHHHHhcchh------HHHHHhcC-CChHHHHHHHHHHhcCCCCCHHHHHHHHHHhCc
Confidence 68888876666665 899999999763 99997654 323344445555444444444566777777765
No 205
>PF02581 TMP-TENI: Thiamine monophosphate synthase/TENI; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2.5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway []. TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group [].; GO: 0004789 thiamine-phosphate diphosphorylase activity, 0009228 thiamine biosynthetic process; PDB: 3NL5_A 3NL2_A 3NM1_A 3NM3_C 3NL6_B 3NL3_A 3CEU_A 3O63_B 3QH2_C 1YAD_D ....
Probab=22.64 E-value=20 Score=29.79 Aligned_cols=69 Identities=22% Similarity=0.289 Sum_probs=38.2
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc-CccccccchhhhhhcccCCccc---------hhhhhhhccccccccc
Q 023705 203 VNLIQLRKASMLDDSQVAEILNEISRRFVREK-DEDALDEQPPMQALFVFDPVHN---------ICCFLHMKWCKRSSCH 272 (278)
Q Consensus 203 aDLi~Lrkas~L~D~evaEiLnE~srRiv~~~-G~vmmn~~~avqalf~~~~~~~---------~~~~~~~~~~~~~~~~ 272 (278)
.++||||.- .+++.+..+..+++.+ +.++| -++++|-..-+=.-++-|-||= .=-.++-.++--.|||
T Consensus 26 v~~v~lR~k-~~~~~~~~~~a~~l~~-~~~~~~~~liin~~~~la~~~~~dGvHl~~~~~~~~~~r~~~~~~~~ig~S~h 103 (180)
T PF02581_consen 26 VDLVQLREK-DLSDEELLELARRLAE-LCQKYGVPLIINDRVDLALELGADGVHLGQSDLPPAEARKLLGPDKIIGASCH 103 (180)
T ss_dssp -SEEEEE-S-SS-HHHHHHHHHHHHH-HHHHTTGCEEEES-HHHHHHCT-SEEEEBTTSSSHHHHHHHHTTTSEEEEEES
T ss_pred CcEEEEcCC-CCCccHHHHHHHHHHH-HhhcceEEEEecCCHHHHHhcCCCEEEecccccchHHhhhhcccceEEEeecC
Confidence 355667765 6788888888888754 45555 4888887632222366666661 1112233455566788
Q ss_pred c
Q 023705 273 E 273 (278)
Q Consensus 273 ~ 273 (278)
.
T Consensus 104 ~ 104 (180)
T PF02581_consen 104 S 104 (180)
T ss_dssp S
T ss_pred c
Confidence 5
No 206
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=22.57 E-value=2.2e+02 Score=22.41 Aligned_cols=64 Identities=23% Similarity=0.292 Sum_probs=39.8
Q ss_pred HHHHHHhCCC---hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccc
Q 023705 170 KGLVQKTGFS---MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALD 240 (278)
Q Consensus 170 k~L~~KTGFs---~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn 240 (278)
+.|..+.||. ..|++|+++.. .--.-+.+.+. |.++-.+.|+-+.+++.+.-..-....| .++|
T Consensus 14 ~~la~~~~~~~is~~~llr~~~~~----~s~~g~~i~~~--l~~g~~vp~~~v~~ll~~~l~~~~~~~g-~ild 80 (151)
T PF00406_consen 14 KRLAKRYGLVHISVGDLLREEIKS----DSELGKQIQEY--LDNGELVPDELVIELLKERLEQPPCNRG-FILD 80 (151)
T ss_dssp HHHHHHHTSEEEEHHHHHHHHHHT----TSHHHHHHHHH--HHTTSS--HHHHHHHHHHHHHSGGTTTE-EEEE
T ss_pred HHHHHhcCcceechHHHHHHHHhh----hhHHHHHHHHH--HHhhccchHHHHHHHHHHHHhhhcccce-eeee
Confidence 5688888885 99999999842 11111334444 4577788888888888776555544444 4444
No 207
>PRK08456 flagellar motor protein MotA; Validated
Probab=22.56 E-value=3.8e+02 Score=24.48 Aligned_cols=54 Identities=9% Similarity=0.087 Sum_probs=41.4
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
.+++.+-++..++|-. -+..|++...=..++++++.+++...- .+||.+.+.+.
T Consensus 76 ~li~~l~~l~~~~r~~----g~laLe~~~~~~~~~fl~~gL~~~~~g--~~~~~i~~~le 129 (257)
T PRK08456 76 ERIKQLVELATLARKD----GVLALEGRVAQIEDEFLKNGLSMLVDG--KDLEEIKESME 129 (257)
T ss_pred HHHHHHHHHHHHhhhh----hHHHHhhcccCcHHHHHHHHHHHhhcC--CCHHHHHHHHH
Confidence 6788888888887652 356777777667789999999987753 38888888876
No 208
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.49 E-value=6.4e+02 Score=23.52 Aligned_cols=57 Identities=19% Similarity=0.181 Sum_probs=41.5
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHH---HHHHHHHhcCCCCChHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVL---RKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~---RKYirY~LnEr~F~pd~VaDLi 206 (278)
.+.+-|.+.+.+.+-.++..+++.|...+|=|+.+++ .+.+.| ..+.-+.+.|.+++
T Consensus 182 el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~--~~~~It~~~v~~~l 241 (363)
T PRK14961 182 KIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINL--GKGNINIKNVTDML 241 (363)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh--cCCCCCHHHHHHHH
Confidence 4555666666676677999999999999998887654 455555 45677888776665
No 209
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=22.42 E-value=26 Score=26.96 Aligned_cols=19 Identities=32% Similarity=0.578 Sum_probs=16.5
Q ss_pred hhhhhhccccccccCCCcC
Q 023705 83 LDLVEFTGSVTQAIPGPRV 101 (278)
Q Consensus 83 ldlveftG~vtQAIPGPRV 101 (278)
.|++|+.|.|++++|+-+.
T Consensus 2 ~~~ie~~G~V~e~L~~~~f 20 (68)
T TIGR00008 2 EDKIEMEGKVTESLPNAMF 20 (68)
T ss_pred CcEEEEEEEEEEECCCCEE
Confidence 4789999999999999854
No 210
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=22.37 E-value=5.1e+02 Score=25.38 Aligned_cols=59 Identities=17% Similarity=0.250 Sum_probs=43.0
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHH---HHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKY---IRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKY---irY~LnEr~F~pd~VaDLi 206 (278)
...+.+.|.+.+.+.+-.++..+++.|...+|-|+..+..-+ +-| ..+..+.+.|.+++
T Consensus 182 ~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~--~~~~It~~~V~~l~ 243 (451)
T PRK06305 182 EETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGL--FPKSLDPDSVAKAL 243 (451)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh--ccCCcCHHHHHHHH
Confidence 345666777777777777999999999999999988776532 223 23558888887655
No 211
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=22.28 E-value=4.7e+02 Score=28.09 Aligned_cols=59 Identities=24% Similarity=0.262 Sum_probs=46.6
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHH---HHHHHHHhcCCCCChHHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVL---RKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~---RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
..+.+-|...+.+++-.++.++|+.|.+.+|=|+-+++ .+-+.|. ....+.+.|.+++.
T Consensus 181 eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLLDqaia~g--~g~It~e~V~~lLG 242 (709)
T PRK08691 181 QQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALG--SGKVAENDVRQMIG 242 (709)
T ss_pred HHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHHhc--CCCcCHHHHHHHHc
Confidence 56777788888888888999999999999999998864 4666663 45678888877643
No 212
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.25 E-value=84 Score=26.30 Aligned_cols=35 Identities=31% Similarity=0.276 Sum_probs=27.7
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023705 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (278)
Q Consensus 198 ~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~ 233 (278)
.++.-..+|.||.--|||-+|||+.|+ +|.|-|+.
T Consensus 136 l~~~~~~~v~l~~~~Gls~~EIA~~lg-iS~~tV~r 170 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEGLSVEEIAERLG-ISERTVRR 170 (185)
T ss_pred cCHHHHHHHHHHHHCCCCHHHHHHHHC-cCHHHHHH
Confidence 455567889999999999999999994 66665543
No 213
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=22.22 E-value=89 Score=32.97 Aligned_cols=59 Identities=20% Similarity=0.305 Sum_probs=33.5
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccchhhhhhcccCCccchhhhhhhccccc
Q 023705 201 LVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQPPMQALFVFDPVHNICCFLHMKWCKR 268 (278)
Q Consensus 201 ~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~~avqalf~~~~~~~~~~~~~~~~~~~ 268 (278)
.+.|++..=---|..-..|-+++-++.++++.+-= ..+-.=||.+||| |||++|----|
T Consensus 295 ~~~~~~s~L~~~gv~~~~i~~lit~i~d~lv~r~l-------eL~~~~~g~~pv~--fcfvvmGS~GR 353 (610)
T COG2905 295 LLDDSLSTLVSRGVRTEFISELITEINDQLVQRAL-------ELVEPEFGAEPVP--FCFVVMGSEGR 353 (610)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH-------HHhhhhhcCCCCc--eEEEEEccCCC
Confidence 34444444344455556666666666666554311 1122348999976 99999964433
No 214
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=22.20 E-value=58 Score=23.21 Aligned_cols=34 Identities=15% Similarity=0.194 Sum_probs=22.4
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCcccc
Q 023705 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKDEDAL 239 (278)
Q Consensus 198 ~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmm 239 (278)
+.+.|.+.++--...|||++||++-+ ++||+=.+
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~--------~~~G~N~l 38 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERR--------KKYGPNEL 38 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHH--------HHHSSSST
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHH--------Hhcccccc
Confidence 44555555554457899998887655 56776555
No 215
>PF03162 Y_phosphatase2: Tyrosine phosphatase family; InterPro: IPR004861 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents protein-tyrosine phosphatases predominantly from fungi, plants and bacteria, several of which are putative enzymes. These proteins are closely related to the Y-phosphatase and DSPc families. This entry includes the PTPase SIW14 from Saccharomyces cerevisiae (Baker's yeast), which plays a role in actin filament organisation and endocytosis.; PDB: 2Q47_A 1XRI_A.
Probab=22.19 E-value=24 Score=29.98 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=23.7
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHHHHHHHhc
Q 023705 161 GDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN 193 (278)
Q Consensus 161 Rdal~~gvLk~L~~KTGFs~~EV~RKYirY~Ln 193 (278)
|.++--+.||.++ |.+.+.|+-.|.||+-+
T Consensus 104 rTG~vvg~lRk~Q---~W~~~~i~~Ey~~f~~~ 133 (164)
T PF03162_consen 104 RTGLVVGCLRKLQ---GWSLSSIFDEYRRFAGP 133 (164)
T ss_dssp HHHHHHHHHHHHT---TB-HHHHHHHHHHHHGG
T ss_pred chhhHHHHHHHHc---CCCHHHHHHHHHHhcCC
Confidence 4555567788664 99999999999999988
No 216
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=22.17 E-value=2.4e+02 Score=24.35 Aligned_cols=35 Identities=29% Similarity=0.397 Sum_probs=15.9
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023705 171 GLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 171 ~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi 206 (278)
.|..+.|++..+|+.+-.+|++. +.|+++...+++
T Consensus 252 ~ll~~~g~~~~~i~~~l~~~~~~-~~~~~~~l~~~~ 286 (319)
T PRK00440 252 DLMIDYGLSGEDIIKQIHREVWS-LDIPEELKVELI 286 (319)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHh-cCCCHHHHHHHH
Confidence 33334455555555444444432 444444444333
No 217
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=22.17 E-value=64 Score=21.77 Aligned_cols=29 Identities=10% Similarity=0.203 Sum_probs=21.2
Q ss_pred CCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023705 195 KPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 195 r~F~pd~VaDLi~Lrkas~L~D~evaEiLn 224 (278)
+.++++.++.++.|. +.|.+-.|||+.++
T Consensus 4 ~~~~~~~~~~i~~l~-~~G~si~~IA~~~g 32 (45)
T PF02796_consen 4 PKLSKEQIEEIKELY-AEGMSIAEIAKQFG 32 (45)
T ss_dssp SSSSHCCHHHHHHHH-HTT--HHHHHHHTT
T ss_pred CCCCHHHHHHHHHHH-HCCCCHHHHHHHHC
Confidence 467787788888887 45699999998875
No 218
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=22.08 E-value=4.9e+02 Score=22.03 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=45.3
Q ss_pred HHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAE 221 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaE 221 (278)
..|+++.|.|..|++++=+.-...+-..+++..+-|..+=+.+|-+|-|--+
T Consensus 75 ~~L~~~~~~~~~~~w~~~~~~~~~~~~L~~~d~e~L~~lg~~LG~~D~~~Q~ 126 (170)
T PF09548_consen 75 ERLEKNEGESFAEAWEEAVEKLLKESALKKEDKEILLELGKSLGYSDREMQE 126 (170)
T ss_pred HHHHcCCCCCHHHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHccCCHHHHH
Confidence 4677888999999999988888888899999999999999999999976544
No 219
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=22.04 E-value=4.6e+02 Score=26.89 Aligned_cols=58 Identities=21% Similarity=0.351 Sum_probs=44.8
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNL 205 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDL 205 (278)
...+.+.|...+.+.+-.++.++++.|.+.+|=|+-+++. +.+.|. ...-|.+.|+++
T Consensus 178 ~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~GdlR~alnlLdqai~~~--~~~It~~~V~~~ 238 (535)
T PRK08451 178 QNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLDQAIIYC--KNAITESKVADM 238 (535)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhc--CCCCCHHHHHHH
Confidence 4567777777788888889999999999999999877654 667776 345677777655
No 220
>PRK12559 transcriptional regulator Spx; Provisional
Probab=22.04 E-value=2.7e+02 Score=22.86 Aligned_cols=64 Identities=14% Similarity=0.245 Sum_probs=41.1
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHH----HHHHHhcCCCCChHHHHHHHHH--------------HhhcCCCcHHHHHH
Q 023705 161 GDAVNPPALKGLVQKTGFSMEDVLRK----YIRYALNEKPFNPDLVVNLIQL--------------RKASMLDDSQVAEI 222 (278)
Q Consensus 161 Rdal~~gvLk~L~~KTGFs~~EV~RK----YirY~LnEr~F~pd~VaDLi~L--------------rkas~L~D~evaEi 222 (278)
.+..+...|+.+-.++|++.++++++ |-.-.+.++..+.+...+++.= +...|.+++++.+.
T Consensus 34 ~~~~s~~el~~~l~~~~~g~~~lin~~~~~~k~l~~~~~~ls~~e~i~ll~~~P~LikRPIi~~~~~~~iGf~~e~~~~~ 113 (131)
T PRK12559 34 SNSMTVDELKSILRLTEEGATEIISTRSKTFQDLNINIEELSLNEFYKLIIEHPLMLRRPIMLDEKRLQIGFNDEEIRKF 113 (131)
T ss_pred CCcCCHHHHHHHHHHcCCCHHHHHhcCcHHHHhCCCCcccCCHHHHHHHHHhCcceEeCCEEEeCCEEEEcCCHHHHHHH
Confidence 46788999999999999999999987 3333333344443333333321 23456667777776
Q ss_pred HH
Q 023705 223 LN 224 (278)
Q Consensus 223 Ln 224 (278)
|.
T Consensus 114 l~ 115 (131)
T PRK12559 114 LP 115 (131)
T ss_pred hh
Confidence 63
No 221
>PRK00767 transcriptional regulator BetI; Validated
Probab=21.82 E-value=4.1e+02 Score=21.10 Aligned_cols=51 Identities=16% Similarity=0.253 Sum_probs=29.9
Q ss_pred ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 023705 179 SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (278)
Q Consensus 179 s~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRi 230 (278)
+..|-++.++.+.+..-.++++.+.-.+.+- +.+..+.++.+.+.+..+++
T Consensus 82 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 132 (197)
T PRK00767 82 TPRARLRAIVEANFDASQFSSPAMKTWLAFW-ASSMHSPDLRRLQRINSRRL 132 (197)
T ss_pred CHHHHHHHHHHHhccHhhcChHHHHHHHHHH-HhccCCHHHHHHHHHHHHHH
Confidence 6778888888876655555565543333332 34555666766665554443
No 222
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=21.73 E-value=1.9e+02 Score=29.18 Aligned_cols=47 Identities=23% Similarity=0.450 Sum_probs=39.9
Q ss_pred cCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH------HhhhhhcCcccc
Q 023705 193 NEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS------RRFVREKDEDAL 239 (278)
Q Consensus 193 nEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s------rRiv~~~G~vmm 239 (278)
.+-+++|+.+++||.|=..-.+|...+.++|.+.. +.|++++|=..+
T Consensus 362 ~~~~i~~~~l~~Li~lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii~~~gl~~i 414 (474)
T PRK05477 362 EESPITPEQLAELIKLIDDGTISGKIAKEVFEEMLETGGDPDEIVEEKGLKQI 414 (474)
T ss_pred hhcCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhcCCCHHHHHHHcCCccc
Confidence 34568999999999999999999999999999884 458888886554
No 223
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=21.71 E-value=96 Score=19.36 Aligned_cols=21 Identities=29% Similarity=0.559 Sum_probs=15.4
Q ss_pred CcCCCCCchhHHhhhhHhhhh
Q 023705 99 PRVGQSKLPWILAVPLAYVGV 119 (278)
Q Consensus 99 PRVg~s~lPwLlAlPLAylG~ 119 (278)
|.-|++...|+..+.++.++.
T Consensus 3 P~TG~~~~~~~~~~G~~l~~~ 23 (34)
T TIGR01167 3 PKTGESGNSLLLLLGLLLLGL 23 (34)
T ss_pred CCCCCcccHHHHHHHHHHHHH
Confidence 566778888888887766654
No 224
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=21.67 E-value=1.3e+02 Score=19.45 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=14.8
Q ss_pred HHHHHHhhcCCCcHHHHHHHH
Q 023705 204 NLIQLRKASMLDDSQVAEILN 224 (278)
Q Consensus 204 DLi~Lrkas~L~D~evaEiLn 224 (278)
-|-.+|+..|++.+|+|+.+.
T Consensus 6 ~l~~~r~~~gltq~~lA~~~g 26 (58)
T TIGR03070 6 LVRARRKALGLTQADLADLAG 26 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHhC
Confidence 355667777888877777764
No 225
>COG0015 PurB Adenylosuccinate lyase [Nucleotide transport and metabolism]
Probab=21.56 E-value=3.9e+02 Score=26.98 Aligned_cols=82 Identities=15% Similarity=0.230 Sum_probs=63.0
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHHHHHHHh-cCCCC------ChHHH--HHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q 023705 161 GDAVNPPALKGLVQKTGFSMEDVLRKYIRYAL-NEKPF------NPDLV--VNLIQLRKASMLDDSQVAEILNEISRRFV 231 (278)
Q Consensus 161 Rdal~~gvLk~L~~KTGFs~~EV~RKYirY~L-nEr~F------~pd~V--aDLi~Lrkas~L~D~evaEiLnE~srRiv 231 (278)
-+..+...+++++.+||-+...+++-+=...- .+..| +.|.+ ++.++||.|..+=..++..+++.++.+-.
T Consensus 54 ~~~~d~~~i~eie~~t~HdV~a~v~~l~e~~~~~~~~~VH~GaTS~DI~Dta~~L~lk~a~~ii~~~l~~l~~~L~~~A~ 133 (438)
T COG0015 54 FAEFDLERIKEIEAETGHDVKALVRALAEKVGEEASEYVHFGATSQDIIDTALALQLKEALDLILPDLKRLIEALAELAL 133 (438)
T ss_pred ccccCHHHHHHHHHHhCCCcHHHHHHHHHhcCcccccceecccchHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678888999999999998887765444444 23323 34433 56799999999999999999999999999
Q ss_pred hhcCccccccc
Q 023705 232 REKDEDALDEQ 242 (278)
Q Consensus 232 ~~~G~vmmn~~ 242 (278)
+-+.++||--.
T Consensus 134 ~~k~t~m~GRT 144 (438)
T COG0015 134 EHKDTPMLGRT 144 (438)
T ss_pred HhCCCeecccc
Confidence 99999998655
No 226
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=21.55 E-value=28 Score=28.24 Aligned_cols=18 Identities=33% Similarity=0.708 Sum_probs=16.1
Q ss_pred hhhhhhccccccccCCCc
Q 023705 83 LDLVEFTGSVTQAIPGPR 100 (278)
Q Consensus 83 ldlveftG~vtQAIPGPR 100 (278)
.|++|+.|.|++.+|+-+
T Consensus 4 e~~ie~~G~V~e~Lp~~~ 21 (87)
T PRK12442 4 EELIELDGIVDEVLPDSR 21 (87)
T ss_pred cceEEEEEEEEEECCCCE
Confidence 589999999999999873
No 227
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=21.49 E-value=2e+02 Score=18.94 Aligned_cols=37 Identities=22% Similarity=0.232 Sum_probs=21.1
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV 183 (278)
+..-++-|..+|..+. -.+......|...+|-+...|
T Consensus 8 ~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~~l~~~qV 44 (56)
T smart00389 8 TPEQLEELEKEFQKNP-YPSREEREELAAKLGLSERQV 44 (56)
T ss_pred CHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHCcCHHHH
Confidence 3444555666666555 356666666666666665444
No 228
>PRK15043 transcriptional regulator MirA; Provisional
Probab=21.40 E-value=2.1e+02 Score=26.63 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=25.9
Q ss_pred HHHHHHhCCChHHHHHHHHH-HHh--------cCCCCChHHHHHHHHHH--hhcCCCcHHHHHHHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIR-YAL--------NEKPFNPDLVVNLIQLR--KASMLDDSQVAEILNE 225 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYir-Y~L--------nEr~F~pd~VaDLi~Lr--kas~L~D~evaEiLnE 225 (278)
++..+.||-+.. -+|.|-+ |-| +.|-|+++.|+-|-.++ +..|++=++|+++|.+
T Consensus 7 geVA~~~GVs~~-TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~ 72 (243)
T PRK15043 7 GEVALLCDINPV-TLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSN 72 (243)
T ss_pred HHHHHHHCcCHH-HHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 344555555543 4455542 433 23445555554443221 3455665666555543
No 229
>PF01369 Sec7: Sec7 domain; InterPro: IPR000904 The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ]. The 3D structure of the domain displays several alpha-helices []. It was found to be associated with other domains involved in guanine nucleotide exchange (e.g., CDC25, Dbl) in mammalian factors [].; GO: 0005086 ARF guanyl-nucleotide exchange factor activity, 0032012 regulation of ARF protein signal transduction, 0005622 intracellular; PDB: 3SWV_A 3L8N_A 2R09_A 2R0D_B 1RE0_B 3LTL_A 1KU1_A 1XSZ_A 1XT0_B 1R8Q_E ....
Probab=21.29 E-value=1.7e+02 Score=25.12 Aligned_cols=38 Identities=18% Similarity=0.386 Sum_probs=21.9
Q ss_pred CCCChHHHHHHHHHHhhcCCCcHHHHHHHHH---HHHhhhhhc
Q 023705 195 KPFNPDLVVNLIQLRKASMLDDSQVAEILNE---ISRRFVREK 234 (278)
Q Consensus 195 r~F~pd~VaDLi~Lrkas~L~D~evaEiLnE---~srRiv~~~ 234 (278)
..=||+.||..+ +...+|+..+|+|.|-. -.+.|.++|
T Consensus 34 ~~~~~~~iA~fL--~~~~~l~k~~ige~Lg~~~~~n~~vL~~y 74 (190)
T PF01369_consen 34 NEDDPKSIAKFL--FQTPGLDKKKIGEYLGKDNPFNRDVLKEY 74 (190)
T ss_dssp S-SSHHHHHHHH--HHTTTS-HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCCHHHHHHHH--HhCCCCCHHHHHHHHhccchHHHHHHHHH
Confidence 344677777776 46667777777777754 334444444
No 230
>PRK09885 putative toxin YafO; Provisional
Probab=21.26 E-value=65 Score=27.89 Aligned_cols=30 Identities=27% Similarity=0.394 Sum_probs=25.8
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHHhhcCCCc
Q 023705 186 KYIRYALNEKPFNPDLVVNLIQLRKASMLDD 216 (278)
Q Consensus 186 KYirY~LnEr~F~pd~VaDLi~Lrkas~L~D 216 (278)
|+||++|++ +-..-+|+|..+-+..-+|.|
T Consensus 8 ~~i~~~~~~-~~~~~l~~df~~YK~~g~lp~ 37 (132)
T PRK09885 8 KLIRLQLTA-EELDALTADFISYKRDGVLPD 37 (132)
T ss_pred hhHHHHhCc-HHHHHHHHHHHHHHcCCCCch
Confidence 889999999 778888999999888877765
No 231
>PF10540 Membr_traf_MHD: Munc13 (mammalian uncoordinated) homology domain; InterPro: IPR019558 Mammalian uncoordinated homology 13 (Munc13) proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana (Mouse-ear cress), C. elegans, Drosophila melanogaster (Fruit fly), Mus musculus (Mouse), Rattus norvegicus (Rat) and Homo sapiens (Human), some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical. ; PDB: 3SWH_A.
Probab=21.25 E-value=64 Score=26.73 Aligned_cols=23 Identities=17% Similarity=0.281 Sum_probs=17.6
Q ss_pred hhHHhhHHHHHhcCCCCCCchHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPAL 169 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvL 169 (278)
-.-.+.|.+||+++++++....|
T Consensus 88 ~~~L~~L~~FFhA~G~Gl~~~~L 110 (137)
T PF10540_consen 88 FKWLDTLKDFFHAEGNGLPLEFL 110 (137)
T ss_dssp HHHHHHHHHHHHCCCTS--HHHH
T ss_pred HHHHHHHHHHHhCCCCCCCHHHH
Confidence 34578889999999999998777
No 232
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=21.23 E-value=84 Score=24.87 Aligned_cols=46 Identities=7% Similarity=0.005 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 023705 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (278)
Q Consensus 185 RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRi 230 (278)
.|.|+=+-.+..+-..+.+|=-++=++.|||++|.+-+++---+.+
T Consensus 7 nrli~~L~~dp~~rerF~~DPea~~~~~gLt~eE~~aL~~~D~~~L 52 (81)
T cd07922 7 NRLIQELFKDPGLIERFQDDPSAVFEEYGLTPAERAALREGTFGAL 52 (81)
T ss_pred HHHHHHHhcCHHHHHHHHHCHHHHHHHcCCCHHHHHHHHccCHHHH
Confidence 4555554444446666677777788899999999987665444433
No 233
>COG2212 MnhF Multisubunit Na+/H+ antiporter, MnhF subunit [Inorganic ion transport and metabolism]
Probab=21.20 E-value=73 Score=25.78 Aligned_cols=39 Identities=18% Similarity=0.473 Sum_probs=29.8
Q ss_pred chhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhh
Q 023705 106 LPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAM 148 (278)
Q Consensus 106 lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VNKNam 148 (278)
+.|++-+.+..+++++.+++||+++-=|.| .|.|.-|..
T Consensus 3 ~~~~~~ial~i~~la~~l~~yRvi~GPt~~----DRvvalD~l 41 (89)
T COG2212 3 LEIMLLIALIILGLALLLALYRVIRGPTLP----DRVVALDTL 41 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCcc----chhhhHhHH
Confidence 568888999999999999999997765544 456555443
No 234
>PRK14952 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.12 E-value=5.2e+02 Score=26.64 Aligned_cols=60 Identities=17% Similarity=0.193 Sum_probs=44.8
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHH---HHHHHHHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMED---VLRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~E---V~RKYirY~LnEr~F~pd~VaDLi 206 (278)
...+.+-|...+.+.+-.++..+++.|.+.+|-|+.+ ++.|++-|.. +..-+.+.|.+++
T Consensus 179 ~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~GdlR~aln~Ldql~~~~~-~~~It~~~v~~ll 241 (584)
T PRK14952 179 PRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAA-DTHVTYQRALGLL 241 (584)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccC-CCCcCHHHHHHHH
Confidence 4567778888888888889999999999999998875 4567777765 3445666665553
No 235
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=21.11 E-value=1.2e+02 Score=29.65 Aligned_cols=82 Identities=23% Similarity=0.272 Sum_probs=61.5
Q ss_pred hhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCC--CchHHHHHHHHhCCChHHHH----HHHHHHHhcCCCCChHHHH
Q 023705 130 KKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAV--NPPALKGLVQKTGFSMEDVL----RKYIRYALNEKPFNPDLVV 203 (278)
Q Consensus 130 rK~~SPraKRkR~VNKNamLvkSLDeyFp~gRdal--~~gvLk~L~~KTGFs~~EV~----RKYirY~LnEr~F~pd~Va 203 (278)
++|-+.+.|| |-.+||+. |-|+|||...+.-- +..+=.+|.+|||.+...|- +|-|||.=|=-.|-++ +
T Consensus 183 ~r~ldarRKR-RNFsK~aT--eiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee--~ 257 (334)
T KOG0774|consen 183 SRFLDARRKR-RNFSKQAT--EILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEE--A 257 (334)
T ss_pred HHHHHHHHhh-cccchhHH--HHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhh--h
Confidence 4566666555 44677774 77999999866543 34566789999999999885 5889999888777554 7
Q ss_pred HHHHHHhhcCCCc
Q 023705 204 NLIQLRKASMLDD 216 (278)
Q Consensus 204 DLi~Lrkas~L~D 216 (278)
||-++|+|-.-+.
T Consensus 258 ~l~~~kk~~~~~~ 270 (334)
T KOG0774|consen 258 NLYAAKKAVDATP 270 (334)
T ss_pred hhHhhcccccCCC
Confidence 9999999876554
No 236
>PF11377 DUF3180: Protein of unknown function (DUF3180); InterPro: IPR021517 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=21.08 E-value=50 Score=27.71 Aligned_cols=38 Identities=16% Similarity=0.196 Sum_probs=23.0
Q ss_pred CchhHHhhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhc
Q 023705 105 KLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVN 144 (278)
Q Consensus 105 ~lPwLlAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VN 144 (278)
++||...+.+..+++--+..-+ .+|++. .+..+++++|
T Consensus 28 ~~p~~~~~~l~~la~~~~~~a~-~vr~~~-~~~~~~~~~~ 65 (138)
T PF11377_consen 28 PIPWTAGVTLLVLAAVELWLAW-QVRRRI-EIGPGRRQLN 65 (138)
T ss_pred CCchHHHHHHHHHHHHHHHHHH-HHHHHH-hcCCCCCCcC
Confidence 5689999999988854444444 456665 3333444433
No 237
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=21.08 E-value=1.1e+02 Score=25.30 Aligned_cols=33 Identities=24% Similarity=0.433 Sum_probs=25.8
Q ss_pred HHHHHhhcC---CCcHHHHHHHHHHHHhhhhhcCcc
Q 023705 205 LIQLRKASM---LDDSQVAEILNEISRRFVREKDED 237 (278)
Q Consensus 205 Li~Lrkas~---L~D~evaEiLnE~srRiv~~~G~v 237 (278)
.|+||..++ .+|+|+..|+.||+.|+=+..+..
T Consensus 31 r~AlKaGL~eieI~d~eL~~~FeeIa~RFrk~~~~~ 66 (92)
T PF07820_consen 31 RIALKAGLGEIEISDAELQAAFEEIAARFRKGKKKQ 66 (92)
T ss_pred HHHHHcccccccCCHHHHHHHHHHHHHHHhcccccc
Confidence 356666654 799999999999999998775543
No 238
>PLN02200 adenylate kinase family protein
Probab=21.07 E-value=3.8e+02 Score=23.71 Aligned_cols=93 Identities=14% Similarity=0.249 Sum_probs=51.8
Q ss_pred cCCCCCCchHH-HHHHHHhCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023705 159 KGGDAVNPPAL-KGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (278)
Q Consensus 159 ~gRdal~~gvL-k~L~~KTGF---s~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~ 234 (278)
-|--+--++.+ +.|.++.|+ |+.|++|+++.. + ...-..+.+. ++++-..+|+.+...+.+.-.. ...+
T Consensus 49 ~G~PGSGKsT~a~~La~~~g~~his~gdllR~~i~~---~-s~~~~~i~~~--~~~G~~vp~e~~~~~l~~~l~~-~~~~ 121 (234)
T PLN02200 49 LGGPGSGKGTQCEKIVETFGFKHLSAGDLLRREIAS---N-SEHGAMILNT--IKEGKIVPSEVTVKLIQKEMES-SDNN 121 (234)
T ss_pred ECCCCCCHHHHHHHHHHHhCCeEEEccHHHHHHHhc---c-ChhHHHHHHH--HHcCCCCcHHHHHHHHHHHHhc-CCCC
Confidence 35556666666 788888887 788999998853 1 1122233443 3445556666666655543322 1233
Q ss_pred Cccccccc-------hhhhhhcccCCccchhh
Q 023705 235 DEDALDEQ-------PPMQALFVFDPVHNICC 259 (278)
Q Consensus 235 G~vmmn~~-------~avqalf~~~~~~~~~~ 259 (278)
| +++|=- .+...+++..|-..|++
T Consensus 122 ~-~ILDG~Prt~~q~~~l~~~~~~~pd~vi~L 152 (234)
T PLN02200 122 K-FLIDGFPRTEENRIAFERIIGAEPNVVLFF 152 (234)
T ss_pred e-EEecCCcccHHHHHHHHHHhccCCCEEEEE
Confidence 3 677653 23334455556555443
No 239
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=20.91 E-value=1.5e+02 Score=20.93 Aligned_cols=53 Identities=23% Similarity=0.310 Sum_probs=32.8
Q ss_pred HHHHHHhCCChHHHHHHHHHH-Hh--------cCCCCChHHHHHHHH---HHhhcCCCcHHHHHHHH
Q 023705 170 KGLVQKTGFSMEDVLRKYIRY-AL--------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILN 224 (278)
Q Consensus 170 k~L~~KTGFs~~EV~RKYirY-~L--------nEr~F~pd~VaDLi~---Lrkas~L~D~evaEiLn 224 (278)
.++.+.+|-+.. -+|.|-+- -| +-|-||++.+..|.. ||. .|++=+||+++|+
T Consensus 4 ~e~A~~~gVs~~-tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l~~-~g~~l~~i~~~l~ 68 (68)
T cd04763 4 GEVALLTGIKPH-VLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWID-NGVQVSKVKKLLS 68 (68)
T ss_pred HHHHHHHCcCHH-HHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHHHhC
Confidence 455556665543 33455432 22 346688887776654 445 8999999998873
No 240
>PF09162 Tap-RNA_bind: Tap, RNA-binding; InterPro: IPR015245 This domain adopts a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. It is mainly found in mRNA export factors, which mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element []. ; GO: 0003723 RNA binding, 0006406 mRNA export from nucleus, 0005634 nucleus, 0005737 cytoplasm; PDB: 1FT8_A 1KOH_C 1KOO_C 3RW6_B 3RW7_C 1FO1_A.
Probab=20.86 E-value=36 Score=27.41 Aligned_cols=23 Identities=26% Similarity=0.486 Sum_probs=20.8
Q ss_pred CCcHHHHHHHHHHHHhhhhhcCc
Q 023705 214 LDDSQVAEILNEISRRFVREKDE 236 (278)
Q Consensus 214 L~D~evaEiLnE~srRiv~~~G~ 236 (278)
.+|.++|++|..+||+|..+-|.
T Consensus 51 V~D~~tA~aLk~vsrkI~~~dg~ 73 (88)
T PF09162_consen 51 VEDASTASALKDVSRKICDEDGF 73 (88)
T ss_dssp ESSHHHHHHHHTTTTTEEBTTSB
T ss_pred eCCHHHHHHHHHCCCceECCCCC
Confidence 57999999999999999998774
No 241
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=20.72 E-value=3.7e+02 Score=22.19 Aligned_cols=16 Identities=13% Similarity=0.245 Sum_probs=6.5
Q ss_pred hcCCCCChHHHHHHHH
Q 023705 192 LNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 192 LnEr~F~pd~VaDLi~ 207 (278)
|++--|+.+.+..++.
T Consensus 54 lr~~G~sL~eI~~~l~ 69 (140)
T PRK09514 54 AKQLGFTLEEIRELLS 69 (140)
T ss_pred HHHcCCCHHHHHHHHH
Confidence 3334444444444443
No 242
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=20.63 E-value=2.2e+02 Score=21.11 Aligned_cols=41 Identities=17% Similarity=0.417 Sum_probs=31.5
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRY 190 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY 190 (278)
..+.+-|.+|...++- ++.+++|....||++.--+.+||.-
T Consensus 9 ~~vL~~I~~~~~~~G~---~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 9 KEVLEFIREYIEENGY---PPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHSS------HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCC---CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 4577888888887654 4689999999999998888888874
No 243
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=20.59 E-value=1.3e+02 Score=28.80 Aligned_cols=44 Identities=30% Similarity=0.323 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023705 181 EDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (278)
Q Consensus 181 ~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srR 229 (278)
..-.|.||=|.+..... ..--.|..+.+|..+++.|||.++|..
T Consensus 335 ~~~aRD~iL~~F~~~~~-----v~r~~l~~~~~l~~~~~~eiL~~~a~~ 378 (421)
T PF04801_consen 335 LCRARDYILLLFTKSRY-----VKRKELMSATKLPPEDVKEILKEIAVL 378 (421)
T ss_pred hhhhHHHHHHHhcCCCc-----eeHHHhhhhcCCCHHHHHHHHHHHhhc
Confidence 44678888888876533 222345589999999999999999984
No 244
>cd07212 Pat_PNPLA9 Patatin-like phospholipase domain containing protein 9. PNPLA9 is a Ca-independent phospholipase that catalyzes the hydrolysis of glycerophospholipids at the sn-2 position. PNPLA9 is also known as PLA2G6 (phospholipase A2 group VI) or iPLA2beta. PLA2G6 is stimulated by ATP and inhibited by bromoenol lactone (BEL). In humans, PNPLA9 in expressed ubiquitously and is involved in signal transduction, cell proliferation, and apoptotic cell death. Mutations in human PLA2G6 leads to infantile neuroaxonal dystrophy (INAD) and idiopathic neurodegeneration with brain iron accumulation (NBIA). This family includes PLA2G6 from Homo sapiens and Rattus norvegicus.
Probab=20.53 E-value=3.1e+02 Score=25.42 Aligned_cols=51 Identities=18% Similarity=0.322 Sum_probs=36.4
Q ss_pred CCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023705 163 AVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 163 al~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~ 226 (278)
+-+.|++=++....|++.+|+..-|.+.. .+-|... ...+...+.++|++.
T Consensus 38 GTStGgiIA~~la~g~s~~e~~~~y~~~~--~~iF~~~-----------~~y~~~~le~~L~~~ 88 (312)
T cd07212 38 GTSTGGILALALLHGKSLREARRLYLRMK--DRVFDGS-----------RPYNSEPLEEFLKRE 88 (312)
T ss_pred eeChHHHHHHHHHcCCCHHHHHHHHHHhh--hhhCCCC-----------CCCCChHHHHHHHHH
Confidence 35788888999889999999999998865 4555432 235566666666653
No 245
>cd05197 GH4_glycoside_hydrolases Glycoside Hydrases Family 4. Glycoside hydrolases cleave glycosidic bonds to release smaller sugars from oligo- or polysaccharides. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by GH4 glycoside hydrolases. Other organisms (such as archaea and Thermotoga maritima) lack the PEP-PTS system, but have several enzymes normally associated with the PEP-PTS operon. GH4 family members include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. They require two cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+), for activity. Some also require reducing conditions. GH4 glycoside hydrolases are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families in
Probab=20.47 E-value=1.2e+02 Score=29.61 Aligned_cols=57 Identities=26% Similarity=0.395 Sum_probs=39.7
Q ss_pred CChHHHHHHHHHHhhcCCC-------cHHHHHHHHHHHHhhhhhcCccccccc---hhhhhhcccCCc
Q 023705 197 FNPDLVVNLIQLRKASMLD-------DSQVAEILNEISRRFVREKDEDALDEQ---PPMQALFVFDPV 254 (278)
Q Consensus 197 F~pd~VaDLi~Lrkas~L~-------D~evaEiLnE~srRiv~~~G~vmmn~~---~avqalf~~~~~ 254 (278)
|+|+.|.||++-...+.++ |++--+...+.++|+++++|.-+ +.+ -.-+||-|-|-|
T Consensus 12 ~tp~li~~l~~~~~~l~~~ei~L~Did~~Rl~~v~~l~~~~~~~~g~~~-~v~~ttD~~~Al~gADfV 78 (425)
T cd05197 12 FTPELVSGLLKTPEELPISEVTLYDIDEERLDIILTIAKRYVEEVGADI-KFEKTMDLEDAIIDADFV 78 (425)
T ss_pred hHHHHHHHHHcChhhCCCCEEEEEcCCHHHHHHHHHHHHHHHHhhCCCe-EEEEeCCHHHHhCCCCEE
Confidence 8999999999887555533 46667789999999999999531 121 334455555544
No 246
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=20.47 E-value=2.9e+02 Score=21.08 Aligned_cols=44 Identities=25% Similarity=0.476 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHHhcCC---CCChHHHHHHHH--HHhhcCCCcHHHHHHHHHH
Q 023705 180 MEDVLRKYIRYALNEK---PFNPDLVVNLIQ--LRKASMLDDSQVAEILNEI 226 (278)
Q Consensus 180 ~~EV~RKYirY~LnEr---~F~pd~VaDLi~--Lrkas~L~D~evaEiLnE~ 226 (278)
..++|.| |.-+.+ ..+.+.+.+++. +.-.-.++++||.+++++.
T Consensus 12 ~i~~F~~---y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~~ 60 (88)
T cd05029 12 LVAIFHK---YSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMEDL 60 (88)
T ss_pred HHHHHHH---HHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Confidence 3444444 455555 566777777663 1123446888888877754
No 247
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.42 E-value=5.2e+02 Score=25.90 Aligned_cols=58 Identities=16% Similarity=0.275 Sum_probs=44.6
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~R---KYirY~LnEr~F~pd~VaDLi 206 (278)
...+.+.|...+.+.+-.++.++++.|...+|=++..+.. |.+.| ..+.|.+.|.+++
T Consensus 177 ~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~---~~~It~~~V~~~l 237 (504)
T PRK14963 177 EEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLAL---GTPVTRKQVEEAL 237 (504)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhc---CCCCCHHHHHHHH
Confidence 3456667777777777778999999999999999988754 55544 5578888887764
No 248
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=20.37 E-value=5.4e+02 Score=27.69 Aligned_cols=60 Identities=18% Similarity=0.233 Sum_probs=44.1
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHH
Q 023705 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLI 206 (278)
Q Consensus 146 NamLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV---~RKYirY~LnEr~F~pd~VaDLi 206 (278)
...|.+.|.+.+.+++-.++..+|+.|...+|-|+-++ +.|.+-|.- ++..+.+.|.+|+
T Consensus 181 ~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~-~~~IT~e~V~all 243 (824)
T PRK07764 181 PEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAG-PEGVTYERAVALL 243 (824)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcC-CCCCCHHHHHHHh
Confidence 45667778888888777789999999999999988654 456665543 4457777766654
No 249
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=20.36 E-value=2.9e+02 Score=23.97 Aligned_cols=61 Identities=15% Similarity=0.287 Sum_probs=39.4
Q ss_pred cCCCCChHHHHHHH-HHHhhcCCCcHHHHHHHHHHHHhhhhhcCccccccc----hhhhhhcccCCc
Q 023705 193 NEKPFNPDLVVNLI-QLRKASMLDDSQVAEILNEISRRFVREKDEDALDEQ----PPMQALFVFDPV 254 (278)
Q Consensus 193 nEr~F~pd~VaDLi-~Lrkas~L~D~evaEiLnE~srRiv~~~G~vmmn~~----~avqalf~~~~~ 254 (278)
++.+|+++-+.+-| +--.+.+++++++.++..++...|+.....- ++.+ ...++|...+.+
T Consensus 57 ~~v~Fd~~KI~~AI~kA~~a~~~~~~~~~~i~~~V~~~l~~~~~~~-IsveEIqDiVE~~L~~~~~~ 122 (154)
T PRK00464 57 RREPFDREKLRRGLRRACEKRPVSSEQIEAAVSRIERQLRASGERE-VPSKEIGELVMEELKKLDEV 122 (154)
T ss_pred cCCCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHcCCCC-CCHHHHHHHHHHHHHhcCCE
Confidence 45789999888855 2222347888999999999999998863211 3333 444555554443
No 250
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=20.23 E-value=2.7e+02 Score=23.78 Aligned_cols=53 Identities=13% Similarity=0.165 Sum_probs=32.0
Q ss_pred CCCchHHHHHHHHhCCChHHHHHHHHHHH------------hcCCCCChHHHHHHHHHHhhcCCCc
Q 023705 163 AVNPPALKGLVQKTGFSMEDVLRKYIRYA------------LNEKPFNPDLVVNLIQLRKASMLDD 216 (278)
Q Consensus 163 al~~gvLk~L~~KTGFs~~EV~RKYirY~------------LnEr~F~pd~VaDLi~Lrkas~L~D 216 (278)
--+...+..+++|.||..-+=+|+||.+. ++..+.....+.....+|+ .||.+
T Consensus 21 lpd~e~I~~~Ee~L~i~lP~eyk~fL~~~s~v~~G~~E~~~i~~~~s~~~l~e~~~~ar~-~glP~ 85 (132)
T PF14567_consen 21 LPDDEQIVEAEEQLGISLPEEYKEFLLEASDVIYGGLEPVGIGDPPSHTYLPEVTADARS-IGLPR 85 (132)
T ss_dssp ---HHHHHHHHHHHT----HHHHHHHHHHTT--BTTB-B-BSS-TTSTTBHHHHHHHHHH-HT--T
T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHHCCCeeecceEEEEEEcCCCcccHHHHHHHHHH-cCCCh
Confidence 34667899999999999999999999864 4444454556666666666 66654
No 251
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.23 E-value=1.6e+02 Score=22.26 Aligned_cols=31 Identities=16% Similarity=0.130 Sum_probs=22.8
Q ss_pred CCCCChHHHHHH---HHHHhhcCCCcHHHHHHHHH
Q 023705 194 EKPFNPDLVVNL---IQLRKASMLDDSQVAEILNE 225 (278)
Q Consensus 194 Er~F~pd~VaDL---i~Lrkas~L~D~evaEiLnE 225 (278)
-|-|+++.|..| ..||. .|++=++|+++|++
T Consensus 37 ~R~Ys~~dv~~l~~I~~Lr~-~G~sl~~i~~~l~~ 70 (88)
T cd01105 37 QRKYSLADVDRLLVIKELLD-EGFTLAAAVEKLRR 70 (88)
T ss_pred ceecCHHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence 366877777655 44554 89999999999874
No 252
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=20.21 E-value=62 Score=25.32 Aligned_cols=53 Identities=17% Similarity=0.180 Sum_probs=42.6
Q ss_pred cCCCcHHHHHHHHHHHHhhhhhcCc----cccccchhhhhhcccCCccchhhhhhhccc
Q 023705 212 SMLDDSQVAEILNEISRRFVREKDE----DALDEQPPMQALFVFDPVHNICCFLHMKWC 266 (278)
Q Consensus 212 s~L~D~evaEiLnE~srRiv~~~G~----vmmn~~~avqalf~~~~~~~~~~~~~~~~~ 266 (278)
-++++++.++++.++++-+.+..|- +|+......+-.|+. -..-|||.|.++-
T Consensus 10 ~~~~~~~~~~~~~~~~~~l~~~lgkPe~~~~v~~~~~~~m~f~g--~~~p~a~v~i~~~ 66 (116)
T PTZ00397 10 VNATDDQADAALSDIENAIADVLGKPLSYIMSGYDYQKHMRFGG--SHDGCCFVRVTSI 66 (116)
T ss_pred CCCccccHHHHHHHHHHHHHHHhCCChHHEEEEEeCCceEEECC--CCCceEEEEEEEe
Confidence 3578888999999999999998876 788888888888883 3457899888753
No 253
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=20.19 E-value=56 Score=27.79 Aligned_cols=40 Identities=15% Similarity=0.330 Sum_probs=21.6
Q ss_pred CCCcCCCCCchhHHhhhhHhhhhhhhhhhhhhhhhcCChh
Q 023705 97 PGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPK 136 (278)
Q Consensus 97 PGPRVg~s~lPwLlAlPLAylG~TFviA~vRtvrK~~SPr 136 (278)
.|||....+-.|-..+...++++.|.+.++-.+|.|-.|-
T Consensus 63 ~g~r~~~~~gewk~v~~~~~~~i~~s~~l~~~~r~~~~~~ 102 (142)
T PF02936_consen 63 TGPRMKAPTGEWKKVFGGVFIFIGFSVLLFIWQRSYVYPP 102 (142)
T ss_dssp -HHHHT---SHHHHHHHHHHHHHHHHHHHHHHHHHHT---
T ss_pred cccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 6778666666776666666666666666666666665544
No 254
>PRK05629 hypothetical protein; Validated
Probab=20.09 E-value=5.2e+02 Score=23.36 Aligned_cols=59 Identities=10% Similarity=0.155 Sum_probs=44.7
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHH---HHHHHHHhcCCCCChHHHHHHHH
Q 023705 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVL---RKYIRYALNEKPFNPDLVVNLIQ 207 (278)
Q Consensus 147 amLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~---RKYirY~LnEr~F~pd~VaDLi~ 207 (278)
..+.+-|.+.+.+.+-.++..+++.|...+|.++.++- .|=+-|. ...-|.+.|.+++.
T Consensus 129 ~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~--~~~It~e~V~~~v~ 190 (318)
T PRK05629 129 RERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDT--QGNVTVEKVRAYYV 190 (318)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC--CCCcCHHHHHHHhC
Confidence 34455699999999988999999999999999998774 4432232 44678888877754
No 255
>PTZ00234 variable surface protein Vir12; Provisional
Probab=20.04 E-value=54 Score=32.64 Aligned_cols=34 Identities=21% Similarity=0.195 Sum_probs=25.1
Q ss_pred hhhHhhhhhhhhhhhhhh--hhcCChhhhhhhhhcc
Q 023705 112 VPLAYVGVSFVIAFVKTV--KKFNSPKFKRKKLVNK 145 (278)
Q Consensus 112 lPLAylG~TFviA~vRtv--rK~~SPraKRkR~VNK 145 (278)
+++|.||+.|.+-.|-+. -|+++||.||||-+=+
T Consensus 369 m~~ailGtifFlfyyn~ss~lks~~~krkrkk~~~e 404 (433)
T PTZ00234 369 VGASIIGVLVFLFFFFKSTPIRSQTNKGEKKKRKPQ 404 (433)
T ss_pred HHHHHHHHHHHhhhhhcccchhccccchhhcccchh
Confidence 467888987777777654 4778899999986433
No 256
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=20.03 E-value=1.5e+02 Score=31.18 Aligned_cols=46 Identities=17% Similarity=0.299 Sum_probs=40.5
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH-------HhhhhhcCcccccc
Q 023705 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS-------RRFVREKDEDALDE 241 (278)
Q Consensus 196 ~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s-------rRiv~~~G~vmmn~ 241 (278)
.++|+.+++|+.|=.--.+|...+.++|.+.. ..|+++||+..++-
T Consensus 518 ~i~~~~l~~l~~~~~~~~is~~~ak~v~~~~~~~~~~~~~~IIee~gl~qiSD 570 (630)
T PRK04028 518 NITDEHIEEVFKLVSEGKIAKEAIEEILKELAENPGKSAEEAAEELGLKGLSE 570 (630)
T ss_pred cCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhcCCCCHHHHHHHhCcccCCH
Confidence 37999999999999999999999999998874 46999999988863
No 257
>PF10408 Ufd2P_core: Ubiquitin elongating factor core; InterPro: IPR019474 This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, (IPR003613 from INTERPRO), which has ligase activity. Ubiquitin conjugation factor E4 is involved in N-terminal ubiquitin fusion degradation proteolytic pathway (UFD pathway). E4 binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin chain assembly in conjunction with E1, E2, and E3. E4 appears to influence the formation and topology of the multi-Ub chain as it enhances ubiquitination at 'Lys-48' but not at 'Lys-29' of the N-terminal Ub moiety.; GO: 0034450 ubiquitin-ubiquitin ligase activity, 0006511 ubiquitin-dependent protein catabolic process, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 2KRE_A 3M63_A 2QIZ_A 2QJ0_A 3M62_A.
Probab=20.03 E-value=1.9e+02 Score=29.17 Aligned_cols=57 Identities=19% Similarity=0.456 Sum_probs=38.2
Q ss_pred HHhCCChHHHHH----HHHHH----------HhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 023705 174 QKTGFSMEDVLR----KYIRY----------ALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (278)
Q Consensus 174 ~KTGFs~~EV~R----KYirY----------~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRi 230 (278)
.|.||+..++++ =|+.. +-.||-|+++.....+..=+-.||-..+.-+-+++.+.|+
T Consensus 557 ~~y~F~P~~ll~~i~~iy~~l~~~~~F~~ava~D~Rsy~~~lf~~a~~~l~~~~l~~~~~i~~f~~l~~~v 627 (629)
T PF10408_consen 557 EKYGFDPKELLSQIVDIYLNLSDSDKFVQAVANDGRSYSPELFEKAVRILRRIGLKSEDEIEKFEELAKKV 627 (629)
T ss_dssp GGGT--HHHHHHHHHHHHHHCTT-HHHHHHHHH-TTT--HHHHHHHHHHHTTSTSSTHHHHHHHHHHCCHH
T ss_pred hhcCCcHHHHHHHHHHHHhhcCCchHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH
Confidence 578898887665 35554 5668999999999998877777876666667777777664
No 258
>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]
Probab=20.00 E-value=2.7e+02 Score=28.76 Aligned_cols=64 Identities=19% Similarity=0.283 Sum_probs=52.5
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023705 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (278)
Q Consensus 148 mLvkSLDeyFp~gRdal~~gvLk~L~~KTGFs~~EV~RKYirY~LnEr~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~s 227 (278)
.=++-|-++|-.|.++.-.++||.|. ..|-|.|-.--+++++++..+ ..|||.+|+.|.-+=.+
T Consensus 386 IPi~YLAnl~tAGdt~pV~~aLkrm~---------amR~Y~Ra~~v~~~~d~~~l~-------~vGlt~~q~eeMYr~lA 449 (513)
T COG1140 386 IPVQYLANLLTAGDTEPVLSALKRML---------AMRHYMRAITVEGKTDTRALE-------EVGLTEAQAEEMYRYLA 449 (513)
T ss_pred chHHHHHHHhhcCCcHHHHHHHHHHH---------HHHHHHHHhhccCccchhHHH-------HcCCCHHHHHHHHHHHH
Confidence 34677888999898888788888775 479999999999999999655 46999999999876555
No 259
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.00 E-value=4e+02 Score=21.00 Aligned_cols=54 Identities=22% Similarity=0.489 Sum_probs=37.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCC--CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcC
Q 023705 169 LKGLVQKTGFSMEDVLRKYIRYALNEK--PFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKD 235 (278)
Q Consensus 169 Lk~L~~KTGFs~~EV~RKYirY~LnEr--~F~pd~VaDLi~Lrkas~L~D~evaEiLnE~srRiv~~~G 235 (278)
...+-..-|.|+.+.+|-|++|..+|+ ||++. .+|++| +++|...=+|+=+-++
T Consensus 16 A~~vl~~lGls~S~Ai~~fl~qi~~~~~iPF~~~------------~~s~ed-~~~l~~~re~~~~~~~ 71 (80)
T PRK11235 16 AYAVLEKLGVTPSEALRLLLQYVAENGRLPFKTV------------LLSDED-AALLETVRERLANPQK 71 (80)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCC------------CCCHHH-HHHHHHHHHHHhCCCC
Confidence 345667889999999999999999998 56643 345543 4455555555544443
Done!